2.22. MedeA Forcefields Bundle: Access to the Most Accurate Forcefields

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This section explains the basics of the interatomic potentials (force fields or forcefields) supported in the MedeA environment. For Forcefields >> Machine Learning Potentials, please see MedeA MLPG: Data Manager for more details.

2.22.1. Selecting a Forcefield

../../_images/FF1.png

To select a specific forcefield, read in a forcefield file from Forcefields >> Read… .

One forcefield file can contain different versions, and most likely you want to use the default version.

../../_images/FF2.png

You can select or verify using a specific variant via Forcefield >> Choose. In this case you want to make sure that you use the additions from Materials Design to pcff:

The initial selection comprises forcefields for:

Organic molecules and polymers

  • pcff.frc
  • pcff+.frc
  • oplsaa.frc
  • oplsaa_extended.frc
  • oplsaa+.frc
  • compass.frc
  • compass+.frc (published part)
  • gaff.frc
  • AUA.frc
  • AUA+.frc
  • trappe+.frc
  • small_molecules+solids.frc

Inorganic compounds

  • inorganic.frc
  • cvff_aug.frc (augmented)
  • bks.frc
  • nacl.frc
  • clayff.frc
  • clayff-dioctahedral.frc
  • clayff-trioctahedral.frc
  • comb3.frc
  • Si-O_JCP2016-comb3.frc
  • AlO_eam_coul.frc
  • CeThUNpPuAmCmO_eam_coul.frc
  • TaO_eam_coul.frc
  • LiS_morse_coul.frc

Semiconductors

  • Tersoff.frc
  • SiO2-Si_Munetoh_2007_Tersoff.frc
  • StillingerWeber.frc
  • ZnCdTeSeHgS_Zhou_2013_StillingerWeber.frc

Metallic systems

  • Zhou_2004.frc
  • Ni_EAM.frc
  • ZrH_v4.frc
  • md-eam.frc
  • EAM_Adams.frc
  • AlMg_Adams_1997.frc
  • AlCu_Cai_1996.frc
  • FeNiCr_Bonny_2011.frc
  • AlCo_Mishin_2013.frc
  • AlNi_Mishin_2009.frc
  • AlTi_Mishin_2003.frc
  • MEAM.frc
  • AlSiMgCuFe_MEAM.frc
  • AuSi_MEAM.frc
  • CH_MEAM.frc
  • Cu_MEAM.frc
  • FeC_MEAM.frc
  • FeTiC_MEAM.frc
  • Ni_MEAM.frc
  • SiC_MEAM.frc
  • W_MEAM.frc

Nist Interatomic Potentials Repository

  • Ag-ATVF^Ag.frc
  • Ag-YM^Ag.frc
  • Al-Fe-MIM^Al-Fe.frc
  • Al-LEA^Al-LEA.frc
  • Al-MDSL^MDSL.frc
  • Al-MIM^Al1.frc
  • Al-Mg-LOARH^mg-al-set.frc
  • Al-Mg-MIM^Al-Mg.frc
  • Al-Pb-LWS^alpb-setfl.frc
  • Al-Sm-Mendelev-2014^Al90Sm10_MendelevM_2014.frc
  • Al-YM2^Al03.frc
  • Al-YM^Al99.frc Au-ATVF^Au.frc
  • Au-GRS05^Au-Grochola-JCP05.frc
  • Co-PM12^Co_PurjaPun_2012.frc
  • Cu-ATVF^Cu.frc
  • Cu-Ag-HW^cu_ag_ymwu.frc
  • Cu-Ag^CuAg.frc
  • Cu-MIM^Cu1.frc
  • Cu-MIM^Mendelev_Cu2_2012.frc
  • Cu-YM^Cu01.frc
  • Cu-Zr^Cu-Zr.frc
  • Cu-Zr^Cu-Zr_2.frc
  • Fe-ATVF^Fe.frc
  • Fe-Cu-Ni-GB^FeCuNi.frc
  • Fe-MIM2^Fe_2.frc
  • Fe-MIM^Fe_5.frc
  • Fe-Ni-Cr-GB-2013^FeNiCr_Bonny_2013_ptDef.frc
  • Fe-Ni-Cr-GB^FeNiCr.frc
  • Fe-Ni-GB^Fe-Ni.frc
  • Fe-P-MIM^Fe-P.frc
  • FeC-GJA^Fe-C_Hepburn_Ackland.frc
  • Mg-MIM^Mg.frc
  • Na-MIM^Na_MendelevM_2014.frc
  • Nb-FPW^Nb.frc
  • Nb-Ti-Al-Farkas-1996^Farkas_Nb-Ti-Al_1996.frc
  • Ni-ATVF^Ni.frc
  • Ni-Al-B2^NiAl02.frc
  • Ni-Al-Co-YM13^Mishin-Al-Co-2013.frc
  • Ni-Al-Co-YM13^Mishin-Ni-Al-Co-2013.frc
  • Ni-Al-Co-YM13^Mishin-Ni-Co-2013.frc
  • Ni-Al-H-AMB^NiAlH_jea.frc
  • Ni-Al-Ni3Al^NiAl.frc
  • Ni-Al-YM09^Mishin-Ni-Al-2009.frc
  • Ni-MIM-2012^Ni1_Mendelev_2012.frc
  • Ni-YM^Ni99.frc
  • Ni-Zr-MIM-2012^Ni-Zr_Mendelev_2012.frc
  • Ni-Zr-MIM-2014^Ni-Zr_Mendelev_2014.frc
  • PdAgH-Hale-2013^PdAgH_HybridPd3Ag.frc
  • PdAgH-Hale-2013^PdAgH_MorsePd3Ag.frc
  • Ru-MIM^Ru.frc
  • Ta-LSAL^newPP1_47-setfl.frc
  • Ta-Ravelo-2013^Ta1_Ravelo_2013.frc
  • Ta-Ravelo-2013^Ta2_Ravelo_2013.frc
  • Ti-Al-RRZ03^Zope-Ti-Al-2003.frc
  • Ti-GJA^Ti.frc
  • U-Mo-Xe-SKS13^U_Mo_Xe.2013.frc
  • V-Fe-MIM^V-Fe.frc
  • W-ATVF^W.frc
  • Zr-MIM2^Zr_2.frc
  • Zr-MIM2^Zr_3.frc
  • Zr-MIM^Zr_1.frc

Noble gases

  • argon_rahman.frc

ReaxFF forcefields

  • AlLiSiO.frc
  • AuOH.frc
  • BaZrYOH.frc
  • CeO.frc
  • CHO.frc
  • CHON.frc
  • CHONFClSi.frc
  • CHONSFPtClNi.frc
  • CHONSMoNi.frc
  • clay_zeolite_water.frc
  • CuClOH.frc
  • CuOH.frc
  • epoxy.frc
  • FeCrOS.frc
  • FeOHCl.frc
  • Generic.frc
  • HONB.frc
  • LiC.frc
  • LiMnO.frc
  • LiPFCHO.frc
  • LiSCFO.frc
  • LiSiCHOF.frc
  • MoS.frc
  • PdCHO.frc
  • protein_water.frc
  • PtCH.frc
  • PtNiCHO.frc
  • PtO.frc
  • TiOH.frc
  • VCHO.frc
  • ZnOH.frc

Mesoscale forcefields

  • Martini.frc
  • Martini-3.0.frc
  • SPICA.frc

Machine Learning Potentials (MLPs)

  • Cu-SNAP.frc
  • Cu_Zuo_JPCA2020.frc
  • Cu-SNAP.frc
  • Ge_Zuo_JPCA2020.frc
  • InP_JCPA2020.frc
  • Li3N-SNAP.frc
  • Li_Zuo_JPCA2020.frc
  • Mo_Zuo_JPCA2020.frc
  • Ni_Zuo_JPCA2020.frc
  • Si_Zuo_JPCA2020.frc
  • Mo-SNAP.frc
  • NbMoTaW-SNAP.frc
  • Ni-SNAP.frc
  • NiMo-SNAP.frc
  • Ta06A.frc
  • WBe_Wood_PRB2019.frc
  • W_2940_2017_2.frc

2.22.2. Assigning Forcefield Parameters and Charges

Right-click in your model window and use Find Forcefield Atom types and Find Forcefield Charges to perform the automatic atom type and partial charge assignment.

../../_images/FF3.png

Note that when using covalent forcefields, it is important to ensure that appropriate bonds and bond orders - single, double, partial-double, and triple - have been set in order for correct atom types to be assigned using the forcefield’s atom template definitions. Failure to use correct bond orders generally results in atoms with incorrect chemical valence, which can give the misleading impression that a forcefield cannot be used for a given molecule. Therefore, if attempts at atom type assignment result in a warning message indicating that the atom type assignment resulted in unknown atom types, you should first ensure that the chemical structures of the molecules in the model are correct.

You may inspect the assignment by clicking on the Spreadsheet Icon icon-spreadsheet, where atom types are listed in the FF Atom Type column (with ‘?’ used to denote any unassigned types). If necessary, the spreadsheet also allows you to change charges and assign any atom type for a selected atom or group of atoms.

../../_images/FF4.png

You can skip the automatic assignment and set all forcefield related values by hand (e.g. to match a publication). In this case, open the spreadsheet and you won’t see the columns FF Atom Type and FF Charge. Insert them by right-clicking in the heading of the spreadsheet and select new columns FF Atom Type and FF Charge.

You can arrange and sort the atoms in the model and assign atom types to groups by selecting more than one field: The selected fields are highlighted in blue, the active field is white. In the example below you can choose one atom type for all four H atoms in Methane.

Setting charges is similar:

  1. Enter charge for the first atom. Click into field and copy with right-click >> Copy FF charge

    ../../_images/FF5.png

  2. Select remaining atoms with mouse and paste with right-click >> Paste to FF charge

    ../../_images/FF6.png

  3. Charge values are copied into the selection

    ../../_images/FF7.png

When using mesoscale systems the forcefield bead types cannot be changed independently. A mesoscale system is built with beads from a particular mesoscale forcefield. Therefore, the forcefield bead type is automatically set at build time. It can be inspected by labeling with Bead labels in the viewer or by clicking on the Spreadsheet Icon icon-spreadsheet for periodic systems, where bead types are listed in the Bead Type column.

2.22.3. Forcefield Overview

2.22.3.1. Organic Molecules and Polymers

We recommend and support the use of pcff+ for all atom molecular dynamics, energy minimization, and related simulations. OPLS-AA, AUA and TraPPE are supplied to use with MedeA GIBBS for computationally efficient configurational space sampling and the use of extended atoms.

All the forcefields for organic systems require topological information (such as bonds and bond orders) to determine the atom type and charge for each atom. These forcefields cannot describe the creation or the breaking of bonds.

2.22.3.1.1. pcff+.frc:

A significant extension to the pcff.frc included with the LAMMPS distribution (see, for example, Sun, Mumby, Maple & Hagler [1]). pcff+.frc preserves the ‘cff-series’ ab-initio based parameters for valence interactions (as used in cff91.frc, cff93.frc and pcff.frc). This is supplemented by a substantial refinement of nonbonded parameters based on high quality experimental data for small molecule liquids and gases, together with new parameterizations for selected compounds such as thiophenes. Details are given in the References section at the end of the file.

Ag Ag Silver metal
Al Al Aluminium metal
Au Au Gold metal
Br Br bromine ion
Cl Cl chlorine ion
Cr Cr Chromium metal
Cu Cu Copper metal
Fe Fe Iron metal
K K Potassium metal
Li Li Lithium metal
Mo Mo Molybdenum metal
Na Na Sodium metal
Ni Ni Nickel metal
Pb Pb Lead metal
Pd Pd Palladium metal
Pt Pt Platinum metal
Sn Sn Tin metal
W W Tungsten metal
Ar ar Argon
Al az aluminium atom in zeolites
Br br bromine atom
C c generic SP3 carbon
C c+ C in guanidinium group
C c- C in charged carboxylate
C c1 sp3 carbon with 1 H 3 heavies
C c2 sp3 carbon with 2 H’s, 2 Heavy’s
C c3 sp3 carbon with 3 hHs 1 heavy
C c3h sp3 carbon in 3-membered ring with hydrogens
C c3m sp3 carbon in 3-membered ring
C c4h sp3 carbon in 4-membered ring with hydrogens
C c4m sp3 carbon in 4-membered ring
C c5 sp2 aromatic carbon in 5-membered ring
C c= non aromatic end doubly bonded carbon
C c=1 non aromatic, next to end doubly bonded carbon
C c=2 non aromatic doubly bonded carbon
C c_0 carbonyl carbon of aldehydes, ketones
C c_1 carbonyl carbon of acid, ester, amide
C c_2 carbonyl carbon of carbamate, urea
C c_a general amino acid alpha carbon (sp3)
Ca ca+ calcium ion
C cg sp3 alpha carbon in glycine
C ci sp2 aromatic carbon in charged imidazole ring (His+)
Cl cl chlorine atom
C co sp3 carbon in acetals
C coh sp3 carbon in acetals with hydrogen
C cp sp2 aromatic carbon
C cr C in neutral arginine
C cs sp2 aromatic carbon in 5 membered ring next to S
C ct sp carbon involved in a triple bond
C cz carbonyl carbon of carbonate
D dw deuterium in heivy water
F f fluorine atom
H h generic hydrogen bound to C, Si,or H
H h* hydrogen bonded to nitrogen, Oxygen
H h+ charged hydrogen in cations
H hb hydrogen atom in bridging hydroxyl group
H hc hydrogen bonded to carbon
He he Helium
H hi Hydrogen in charged imidazole ring
H hn hydrogen bonded to nitrogen
H hn2 amino hydrogen
H ho hydrogen bonded to oxygen
H ho2 hydroxyl hydrogen
H hoa hydrogen atom in terminal hydroxyl group on aluminium
H hos hydrogen atom in terminal hydroxyl group on silicon
H hp hydrogen bonded to phosphorus
H hs hydrogen bonded to sulfur
H hsi silane hydrogen
H hw hydrogen in water
I i iodine atom
Kr kr Krypton
N n generic sp2 nitrogen (in amids))
N n+ sp3 nitrogen in protonated amines
N n1 sp2 nitrogen in charged arginine
N n2 sp2 nitrogen (NH2) in guanidinium group (HN=C(NH2)2)
N n3m sp3 nitrogen in 3- membered ring
N n3n sp2 nitrogen in 3- membered ring
N n4 sp3 nitrogen in protonated amines
N n4m sp3 nitrogen in 4- membered ring
N n4n sp2 nitrogen in 4- membered ring
N n= non aromatic end doubly bonded nitrogen
N n=1 non aromatic, next to end doubly bonded carbon
N n=2 non aromatic doubly bonded nitrogen
N n_2 nitrogen of urethane
N na sp3 nitrogen in amines
N nb sp2 nitrogen in aromatic amines
Ne ne Neon
N nh sp2 nitrogen in 5 or 6 membered ring
N nh+ protonated nitrogen in 6 membered ring
N nho sp2 nitrogen in 6 membered ring next to a carbonyl
N ni nitrogen in charged imidazole ring
N nn sp2 nitrogen in aromatic amines
N np sp2 nitrogen in 5- or 6- membered ring
N npc sp2 nitrogen in 5- or 6- membered ring and with a heavy atom
N nr sp2 nitrogen (NH2) in guanidinium group (HN=C(NH2)2)
N nt sp nitrogen involved in a triple bond
N nz sp3 nitrogen bonded to two atoms
O o generic SP3 oxygen
O o* oxygen in water
O o- partial double oxygen
O o3e sp3 oxygen in three membered ring
O o4e sp3 oxygen in four membered ring
O o= oxygen double bonded to O, C, S, N, P
O o_1 oxygen in carbonyl group
O o_2 ester oxygen
O oah oxygen atom in terminal hydroxyl group on aluminium
O oas oxygen atom between aluminium and silicon
O ob oxygen atom in bridging hydroxyl group
O oc sp3 oxygen in ether or acetals
O oe sp3 oxygen in ester
O oh oxygen bonded to hydrogen
O oo oxygen in carbonyl group, carbonate only
O op sp2 aromatic in 5 membered ring
O osh oxygen atom in terminal hydroxyl group on silicon
O osi siloxane oxygen
O oss oxygen atom between two silicons
O oz ester oxygen in carbonate
P p general phosphorous atom
P p= phosphazene phosphorous atom
S s sp3 sulfur
S s’ S in thioketone group
S s- partial double sulfur
S s1 sp3 sulfur involved in (S-S) group of disulfides
S s3e sulfur in three membered ring
S s4e sulfur in four membered ring
S sc sp3 sulfur in methionines (C-S-C) group
S sf S in sulfonate group
S sh sp3 sulfur in sulfhydryl (-SH) group (e.g. cysteine)
Si si silicon atom
Si sio siloxane silicon
S sp sulfur in an aromatic ring (e.g. thiophene)
Si sz silicon atom in zeolites
Xe xe Xenon
As as Arsenic in AsR3
B b3n sp2 boron in hexagonal boron nitride
Br brh bromine in HBr molecule
C c0 sp3 carbon with 0 H, 4 heavies
C c0x sp3 carbon with 0 H, 4 fluorines
C c1o carbon in CO
C c2= carbon in CO2 and CS2
C c3as sp3 carbon in methyl arsines
C c3h1 sp3 carbon in 3-membered ring with one hydrogen
C c3si sp3 carbon with 3 hydrogens and Si
C c3o- carbon in carbonate anion
C c41o carbon, sp3, in methanol
C c43o carbon, sp3 in secondary alcohols
C c4h1 sp3 carbon in 4-membered ring with one hydrogen
C c4o alpha carbon
C c0oe alpha carbon in ether containing tertiary alkyl group, e.g. -C-O-C-R3
C c1oe alpha carbon in ether containing secondary alkyl group, e.g. -C-O-CH-R2
C c2oe alpha carbon in ether containing primary alkyl group, -C-O-CH2-R
C c2oz alpha carbon in carbonates -O(O)C-O-CH2-R
C c3oe alpha carbon in methyl containing ethers -C-O-CH3
C c3oz alpha carbon in methyl-containing carbonates -O(O)C-O-CH3
C c4oe alpha carbon in general ethers -C-O-C- (legacy)
C c5h sp3 carbon in 5-membered ring
C c5h1 sp3 carbon in 5-membered ring with one hydrogen
Cl cl4 chlorine in ClO4- anion
Cl clh chlorine in HCl molecule
C cpc alpha/ipso carbon in aromatic ethers -C-O-C-
Cs Cs+ cesium ion
F ff fluorine atom in perfluorinated aliphatics
F ffp fluorine atom in perfluorinated aromatics
F F fluorine ion
Ge ge4 generic germanium with four bonds attached
H h1h hydrogen in H2
H h_1p hydrogen in NH4+
H hbr hydrogen in HBr molecule
H hcl hydrogen in HCl molecule
H hhi hydrogen in HI molecule
H ho- hydrogen in hydroxide ion OH-
I I iodine ion
I ih iodine in HI molecule
K K+ potassium ion
Li Li+ lithium ion
N n1o nitrogen in NO
N n2o nitrogen in NO2
N n2- nitrogen in amide/imide anion
N n3b sp2 nitrogen in hexagonal boron nitride
N n4o nitrogen in amine oxides
N n_3 nitrogen in primary or secondary amide
N n_3- nitrogen in NO3- nitrate ion
N n_30 nitrogen in tertiary amide
N n_31 nitrogen in secondary amide
N n_32 nitrogen in primary amide
N n_4 nitrogen in NH4+
N n_4c nitrogen in NR4+
N na0 sp3 nitrogen in tertiary aliphatic amines
N na1 sp3 nitrogen in secondary aliphatic amines
N na2 sp3 nitrogen in primary aliphatic amines (same as na)
N nbo sp2 nitrogen in aromatic nitro compounds
Na Na+ sodium ion
O o=n oxygen double bonded to N in aromatic nitro group
O o1= oxygen in NO2 and SO2
O o1=* oxygen in CO2
O o1c oxygen in CO
O o1c- oxygen in carbonate anion
O o1n oxygen in NO
O o1n4 oxygen in amine oxides
O o1o oxygen in O2
O o1s- oxygen in sulfate or sulfonate anion
O o1n- oxygen in nitrate ion
O o2s- ether oxygen in sulfate anion
O o_1h oxygen in carbonyl group of aldehydes
O o_1r oxygen in ClO4- anion
O o_2c oxygen in carboxylic acids
O oc sp3 oxygen in ether or acetals
O oh- oxygen in hydroxide ion OH-
P p6- phosphorous in phosphate
P ph3 phosphorous in phosphine
Rb Rb+ rubidium ion
S s1= sulfur in CS2
S s2= sulfur in SO2
S se- sulfur in sulfate anion

2.22.3.1.2. oplsaa+.frc

Based on Jorgensen, Maxwell & Tirado-Rives [2] (oplsaa), supplemented with inclusion of additional parameters derived by various groups (oplsaa_extended), and original work by Materials Design (oplsaa+).

Ar Ar Argon atom
C C Carbonyl carbon in amides, esters
C CA Aromatic carbon
C CAh1 Aromatic carbon pyridine atom 2
C CAh2 Aromatic carbon pyridine atom 3
C CAh3 Aromatic carbon pyridine atom 4
C CAh4 Aromatic carbon pyrimidine atom 3
C CAh5 Aromatic carbon pyrimidine atom 4
C CAh6 Aromatic carbon pyridazine atom 2
C CAh7 Aromatic carbon pyridazine atom 3
C CAh8 Aromatic carbon pyrazine
C CAh9 Aromatic carbon pyrazole
C CAh0 Aromatic carbon isoxazole
C CAi1 Aromatic carbon indole atom 4
C CAi2 Aromatic carbon indole atom 5
C CAi3 Aromatic carbon indole atom 6
C CAi4 Aromatic carbon indole atom 7
C CB Aromatic carbon indole atom 9
C CM sp2 aliphatic carbon
C CN aromatic carbon indole atom 8
C CO Acetal carbon ROCOR
C CQ pyrimidine N-C-N aromatic carbon
C CR Aromatic carbon imidazole
C CRh1 Aromatic carbon oxazole
C CS Generic 5-membered ring carbon
C CSh1 Aromatic carbon pyrrole
C CSh2 Aromatic carbon furan
C CSh3 Aromatic carbon indole atom 3
C CT sp3 aliphatic carbon
C CT1 sp3 alpha carbon in nitriles
C CTEX Exocyclic sp3 aliphatic carbon in cyclic amine
C CTfn Perfluoroalkane carbon
C CTf4 Tetrafluoromethane carbon
C CU Aromatic carbon pyrazole
C CUh1 Aromatic carbon isoxazole
C CV Aromatic carbon imidazole
C CVh1 Aromatic carbon oxazole
C CW sp2 aliphatic carbon
C CWh1 Aromatic carbon pyrrole
C CWh2 Aromatic carbon furan
C CWh3 Aromatic carbon pyrazole
C CWh4 Aromatic carbon isoxazole
C CWh5 Aromatic carbon imidazole
C CWh6 Aromatic carbon oxazole
C CWh7 Aromatic carbon indole atom 2
C CZ sp alkyl nitrile carbon
C CZ1 sp aryl nitrile carbon
F F Fluorine in perfluorinated hydrocarbons
H H Amide or amine H(N) hydrogen
H HA Aromatic hydrogen
H HC Hydrogen bonded to carbon
H HC1 Hydrogen bonded to carbon in methanol
H HC2 Hydrogen bonded to carbon in alkenes RH-C= and H2-C=
H HC3 Hydrogen bonded to carbon in ethers
H HC4 Hydrogen bonded to carbon next to NR2, NO2, or nitrile
H HC5 alpha alkoxy H in esters
H HC6 H on alpha carbon of aldehyde and ketone
He He Helium atom
H HEX4 Amine hydrogen in 4-membered cyclic amine (azetidine)
H HEX5 Amine hydrogen in 5-membered cyclic amine (pyrrolidine)
H HEX6 Amine hydrogen in 6-membered cyclic amine (piperidine)
H HW Hydrogen in TIP3P water
H HO Hydrogen bonded to O
H HS Hydrogen bonded to S in thiols
Kr Kr Krypton atom
N N Nitrogen in amides
N N1 Nitrogen in primary amides
N N2 Nitrogen in secondary amides
N N3 Nitrogen in tertiary amides
Ne Ne Neon atom
N NA Nitrogen in pyrrole
N NAh2 N-H Nitrogen in pyrazole
N NAh3 N-H Nitrogen in imidazole
N NAh4 N-H Nitrogen in indole (atom 1)
N NB Nitrogen in pyrazole
N NBh1 Nitrogen in isoxazole
N NBh2 Nitrogen in imidazole
N NBh3 Nitrogen in oxazole
N NC Nitrogen in pyridine and diazenes
N NO Nitrogen in nitroalkane
N NT0 Nitrogen in ammonia
N NT Nitrogen in primary amines
N NT2 Nitrogen in secondary amines
N NT3 Nitrogen in tertiary amines
N NZ Nitrogen in nitriles
O O Oxygen in amides
O O1 Oxygen in carboxylate esters
O O2 Oxygen in aldehydes
O O3 Oxygen in ketones
O O4 Oxygen in carboxylic acids RCOOH
O OH Oxygen in hydroxyl (OH) group
O OH2 Oxygen in hydroxyl (OH) group (diols)
O OH3 Oxygen in hydroxyl (OH) group (triols)
O OH4 Oxygen in hydroxyl (OH) group (RCOOH)
O OH5 Oxygen in hydroxyl (OH) group (phenol)
O ON Oxygen in nitro group
O OS Oxygen in ethers, including acetals
O OS1 Alkoxy oxygen in esters
O OW Oxygen in TIP3P water
S S Sulfur in sulfides and disulfides
S SH Sulfur in thiols
S SH1 Sulfur in H2S
Xe Xe Xenon atom
C C1i aliphatic carbon bonded to N in R4N+
C C2i aliphatic carbon bonded to C1i in R4N+
C CTi sp3 aliphatic carbon in ionic liquid
F Fi Fluorine in ionic liquid anion
H H1 Hydrogen bonded to C1 in R4N+ cation
N N2i Nitrogen bonded to S in triflimide anion
N N4i Nitrogen in R4N+ cation
O OYi Oxygen bonded to S in triflate
S SY6i Sulfur in bis triflimide

2.22.3.1.3. Trappe+.frc

Martin [3] , Kamath [4] , Stubbs [5] , Wick [6] , Chen [7] , Wick [8] , Martin [9] , Lubna [10] , Maerzke [11]

C C Aliphatic
C CHx-aliphatic Aliphatic
C CH4-TraPPE-UA Molecule CH4-TraPPE-UA
C CH3-TraPPE-UA Group CH3-TraPPE-UA-
C CH2-TraPPE-UA Group CH2-TraPPE-UA-
C CH-TraPPE-UA Group CH-TraPPE-UA-
C C-TraPPE-UA Group C-TraPPE-UA-
C CH2-olef-TraPPE-UA Group CH2-olef-TraPPE-UA=
C CH-olef-TraPPE-UA Group CH-olef-TraPPE-UA=
C C-olef-TraPPE-UA Group C-olef-TraPPE-UA=
C CH-EA-TraPPE-UA Group CH-EA-TraPPE-UA- for C bonded to O in Ethers and Alcohols
C CH-(EA)-TraPPE-UA Group CH-EA-TraPPE-UA- for C bonded to O in Ethers and Alcohols
C C-EA-TraPPE-UA Group C-EA-TraPPE-UA- for C bonded to O in Ethers and Alcohols
C C-(EA)-TraPPE-UA Group C-EA-TraPPE-UA- for C bonded to O in Ethers and Alcohols
C C-arom-TraPPE-UA Aromatic C-arom-TraPPE-UA carbon
C C-l-arom-TraPPE-UA Aromatic C-arom-TraPPE-UA carbon linking two rings in condensed units (naphthalene, indane, phenanthrene,.. )
C C-d-arom-TraPPE-UA Aromatic C-arom-TraPPE-UA carbon linking two rings in diphenyl
C CH-arom-TraPPE-UA Aromatic C-arom-TraPPE-UA carbon with one hydrogen
C CH-aldehyde-TraPPE-UA C connected to O in aldehydes TraPPE-UA
C CH-(aldehyde)-TraPPE-UA C connected to O in aldehydes TraPPE-UA
C C-ketone-TraPPE-UA C connected to O in ketones TraPPE-UA
C C-(ketone)-TraPPE-UA C connected to O in ketones TraPPE-UA
C CH2-cyc5-TraPPE-UA Group CH2- in a 5-membered cyclic non-aromatic ring
C CH2-cyc6-TraPPE-UA Group CH2- in a 6-membered cyclic non-aromatic ring
C CH-cyc-TraPPE-UA Group CH- in a 5- or 6-membered cyclic non-aromatic ring
C C-cyc-TraPPE-UA Group C- in a 5- or 6-membered cyclic non-aromatic ring
H H-OH-TraPPE-UA Hydrogen bonded to O in OH groups
H H(-OH)-TraPPE-UA Hydrogen bonded to O in OH groups
H HA Aromatic hydrogen
H UnitedH ghost H (used also for aromatic in this version)
H H-SH-TraPPE-UA H bonded with S in thiols
H H-pyrrole-TraPPE-UA H bonded with N in pyrrole
N N-pyridine-TraPPE-UA Nitrogen in pyridine
N N-pyrrole-TraPPE-UA Nitrogen in pyrrole
N N-arom-TraPPE-UA Nitrogen in aromatic rings
O O-OH-TraPPE-UA Oxygen in hydroxyl (O-OH-TraPPE-UA) group
O O(-OH)-TraPPE-UA Oxygen in hydroxyl (O-OH-TraPPE-UA) group
O O-ROR-TraPPE-UA Oxygen in ethers
O O(ROR)-TraPPE-UA Oxygen in ethers
O O-aldehydeketone-TraPPE-UA Oxygen in aldehydes and ketones TraPPE-UA
O O-(aldehydeketone)-TraPPE-UA Oxygen in aldehydes and ketones TraPPE-UA
S S Sulfur
S S-thiol-TraPPE-UA Sulfur in thiols
S S-sulfide-TraPPE-UA Sulfur in sulfides
S S-disulfide-TraPPE-UA Sulfur in disulfides
S S-thiophene-TraPPE-UA Sulfur in thiophene

2.22.3.1.4. compass+.frc - The Published Part of COMPASS

Supplied for consistency with the LAMMPS distribution. General use of this forcefield is deprecated, as the forcefield is not maintained. [12] Contains the collection of compass parameters in their original published form. compass+.frc includes subsequently published corrections.

2.22.3.1.5. Cvff.frc

Supplied for consistency with the LAMMPS distribution. General use of this forcefield is deprecated. [13]

2.22.3.1.6. Cff91.frc

Supplied for consistency with the LAMMPS distribution. General use of this forcefield is deprecated. [14]

2.22.3.1.7. Cff93.frc

Supplied for consistency with the LAMMPS distribution. General use of this forcefield is deprecated. [15]

2.22.3.2. Inorganic Compounds

We don’t make overall recommendations for inorganic forcefields, because the local coordination of inorganic systems varies widely, and the transferability of forcefield terms cannot be assumed from one compound to another. The scope and applicability of forcefields for inorganics are best discerned through reference to their original derivation. These forcefields don’t require bonds.

2.22.3.2.1. inorganic.frc

Compiled by Woodley, Battle, Gale & Catlow [16], Xia [17] for use in inorganic crystal structure prediction.

Ag Ag1+  
Ag Ag3+  
Al Al3+  
Ba Ba2+  
Ca Ca2+  
Cd Cd2+  
Ce Ce4+  
Co Co2+  
Co Co3+  
Cr Cr3+  
Cu Cu1+  
Fe Fe2+  
Fe Fe3+  
Ge Ge4+  
K K1+  
La La3+  
Mg Mg2+  
Mn Mn2+  
Mn Mn4+  
Na Na1+  
Nb Nb5+  
Ni Ni2+  
O O2-  
O O12-  
O O22-  
Pb Pb1+  
Po Po4+  
Pr Pr3+  
Rb Rb1+  
Si Si4+  
Sn Sn4+  
Sr Sr2+  
Ta Ta2+  
Tl Tl3+  
Ti Ti3+  
Ti Ti4+  
U U2+  
V V2+  
V V3+  
V V4+  
Y Y3+  
Zn Zn2+  
Zr Zr2+  

2.22.3.2.2. bks.frc

Derived by van Beest, Kramer & van Santen [18] to provide a description of structural and vibrational properties for framework structure materials based on two-body (i.e. without explicit angle terms).

Al Al  
O O  
P P  
Si Si  

2.22.3.2.3. CVFF_aug.frc

This forcefield was developed by Behnam Vessal using a methodology similar to that employed by van Beest, to create a broad two-body (i.e. without explicit angle terms) description of framework structured materials able to support extra framework atoms. [19]

H h Hydrogen bonded to C. Masses from CRC 1973/74 pages B-250.
H d General Deuterium
H hn Hydrogen bonded to N
H ho Hydrogen bonded to O
H hp Hydrogen bonded to P
H hs Hydrogen bonded to S
H h* Hydrogen in water molecule
H h$ Hydrogen atom for automatic parameter assignment
L lp Lone Pair
L lp Lone Pair
H h+ Charged hydrogen in cations
H hc Hydrogen bonded to carbon
H hi Hydrogen in charged imidazole ring
H hw Hydrogen in water
D dw Deuterium in heivy water
C c Sp3 aliphatic carbon
C cg Sp3 alpha carbon in glycine
C c’ Sp2 carbon in carbonyl (C=O) group
C c* Carbon in carbonyl group, non_amides
C c” Carbon in carbonyl group, non_amides
C cp Sp2 aromatic carbon (partial double bonds)
C cr Carbon in guanidinium group (HN=C(NH2)2)
C c+ C in guanidinium group
C c- Carbon in charged carboxylate (COO-) group
C ca General amino acid alpha carbon (sp3)
C c3 Sp3 carbon in methyl (CH3) group
C cn Sp3 Carbon bonded to N
C c2 Sp3 carbon bonded to 2 H’s, 2 heavy atoms
C c1 Sp3 carbon bonded to 1 H, 3 Heavy atoms
C c5 Sp2 aromatic carbon in five membered ring
C cs Sp2 carbon involved in thiophene
C c= Non aromatic end doubly bonded carbon
C c=1 Non aromatic, next to end doubly bonded carbon
C c=2 Non aromatic doubly bonded carbon
C ct Sp carbon involved in triple bond
C ci Sp2 aromatic carbon in charged imidazole ring (His+)
C c$ Carbon atom for automatic parameter assignment
C co Sp3 carbon in acetals
C c3m Sp3 carbon in 3-membered ring
C c4m Sp3 carbon in 4-membered ring
C coh Sp3 carbon in acetals with hydrogen
C c3h Sp3 carbon in 3-membered ring with hydrogens
C c4h Sp3 carbon in 4-membered ring with hydrogens
C ci Sp2 aromatic carbon in charged imidazole ring (His+)
N n Sp2 nitrogen with 1 H, 2 heavy atoms (amide group)
N no Sp2 nitrogen in nitro group
N n2 Sp2 nitrogen (NH2 in the guanidinium group (HN=C(NH2)2))
N np Sp2 aromatic nitrogen (partial double bonds)
N n3 Sp3 nitrogen with three substituents
N n4 Sp3 nitrogen with four substituents
N n= Non aromatic end double bonded nitrogen
N n=1 Non aromatic, next to end doubly bonded carbon
N n=2 Non aromatic doubly bonded nitrogen
N nt Sp nitrogen involved in triple bond
N nz Sp nitrogen in N2
N n1 Sp2 nitrogen in charged arginine
N ni Sp2 nitrogen in a charged imidazole ring (HIS+)
N n$ Nitrogen atom for automatic parameter assignment
N na Sp3 nitrogen in amines
N n3m Sp3 nitrogen in 3- membered ring
N n4m Sp3 nitrogen in 4- membered ring
N n3n Sp2 nitrogen in 3- membered ring
N n4n Sp2 nitrogen in 4- membered ring
N nb sp2 nitrogen in aromatic amines
N nn sp2 nitrogen in aromatic amines
N npc sp2 nitrogen in 5- or 6- membered ring bonded to a heavy atom
N nh sp2 nitrogen in 5-or 6- membered ring with hydrogen attached
N nho sp2 nitrogen in 6- membered ring next to a carbonyl group and with a hydrogen
N nh+ protonated nitrogen in 6- membered ring with hydrogen attached
N n+ sp3 nitrogen in protonated amines
N nr sp2 nitrogen (NH2) in guanidinium group (HN=C(NH2)2)
O o’ Oxygen in carbonyl (C=O) group
O o sp3 oxygen in ether or ester groups
O o- Oxygen in charged carboxylate (COO-) group
O oh Oxygen in hydroxyl (OH) group
O o* Oxygen in water molecule
O op Oxygen in aromatic rings. e.g. furan
O of Oxygen in
O o$ Oxygen atom for automatic parameter assignment
O oc sp3 oxygen in ether or acetals
O oe sp3 oxygen in ester
O o3e sp3 oxygen in three membered ring
O o4e sp3 oxygen in four membered ring
S s Sulfur in methionine (C-S-C) group
S s1 Sulfur involved in S-S disulfide bond
S sh Sulfur in sulfhydryl (-SH) group
S sp Sulfur in thiophene
S s’ Sulfur in thioketone (>C=S) group
S s$ Sulfur atom for automatic parameter assignment
S sc sp3 sulfur in methionines (C-S-C) group
S s3e Sulfur in three membered ring
S s4e Sulfur in four membered ring
S s- Sulfur bonded to something then bonded to another partial double O or S
P p General phosphorous atom
P p$ Phosphorous atom for automatic parameter assignment
Ca ca+ Calcium ion - Ca++, mass = mass of Ca - 2*electron mass.
F f Fluorine bonded to a carbon
Cl cl Chlorine bonded to a carbon
Br br Bromine bonded to a carbon
I i Covalently bound Iodine
Si si Silicon atom (General)
H nu NULL atom for relative free energy
Cl Cl Chloride ion Cl-
Br Br Bromide ion Br-
Na Na Sodium metal
Ar ar Argon
Si sz Silicon atom in zeolites
Si sy Tetrahedral Silicon atom in Clays
O oz Oxygen atom in zeolites
O oy Oxygen atom in Clays
Al az Tetrahedral Aluminum atom in zeolites
Al ay Octahedral Aluminum atom in Clays
Al ayt Tetrahedral Aluminum atom to be used with oy
P pz Phosphorous atom in zeolites
P py Phosphorous atom to be used with oy
Ga ga Gallium atom in zeolites
Ge ge Germanium atom in zeolites
Ti tioc Titanium (Octahedral) in zeolites
Ti ti4c Titanium (Octahedral) to be used with oy
Ti titd Titanium (Tetrahedral) in zeolites
Li li+ Lithium ion in zeolites
Li lic+ Lithium ion to be used with oy in Clays
Li lioh Lithium ion in water to be used with o*
Na na+ Sodium ion in zeolites
Na nac+ Sodium ion in Clays
Na naoh Sodium ion in water to be used with o*
K k+ Potassium ion in zeolites
K koh Potassium ion in water to be used with o*
Rb rb+ Rubidium ion in zeolites
Cs cs+ Cesium ion in zeolites
N nh4+ United atom type for ammonium ion to be used with oy
Mg mg2+ Magnesium ion in zeolites
Mg mg2c Octahedral Magnesium ion in Clays
Mn mn4c Manganese (IV) ion to be used with oy in Clays
Mn mn3c Manganese (III) ion to be used with oy in Clays
Co co2c Cobalt (II) ion to be used with oy in Clays
Ni ni2c Nickel (II) ion to be used with oy in Clays
Ca ca2+ Calcium ion in zeolites
Ca ca2c Calcium ion to be used with oy in Clays
Sr sr2c Strontium ion to be used with oy in Clays
Ba ba2+ Barium ion in zeolites
Cu cu2+ Copper(II) ion in zeolites
Fe fe2c Octahedral Fe(II) ion in clays
F f- Fluoride ion in zeolites
Be beoh Beryllium (II) in water to be used with o*
F foh Fluoride ion in water to be used with o*
Cl cl- Chloride ion in zeolites
Cl cloh Chloride ion in water to be used with o*
Cl cly- Chloride ion to be used with oy in Clays
Br br- Bromide ion in zeolites
I i- Iodide ion in zeolites
S so4 Sulfur in sulphate ion to be used with oz
S so4y Sulfur in sulphate ion to be used with oy in Clays
H hocl Hydrogen in hydroxyl group in Clays
Pd pd2+ Palladium(II)
V vy Tetrahedral Vanadium to be used with oy
Al al Aluminium metal
Na Na Sodium metal
Pt Pt Platinum metal
Pd Pd Palladium metal
Au Au Gold metal
Ag Ag Silver metal
Sn Sn Tin metal
K K Potassium metal
Li Li Lithium metal
Mo Mo Molybdenum metal
Fe Fe Iron metal
W W Tungsten metal
Ni Ni Nickel metal
Cr Cr Chromium metal
Cu Cu Copper metal
Pb Pb Lead metal

2.22.3.2.4. Nacl.fr

This forcefield provides an illustration of the incorporation of a general inorganic forcefield description in the MedeA environment framework.

Na Na1+ sodium atom
Cl Cl1- chlorine atom

2.22.3.2.5. Clayff.frc

Also applies to clayff-dioctahedral.frc and clayff-trioctahedral.frc.

H h* water hydrogen
H ho H hydroxyl hydrogen
O o* water oxygen
O oh hydroxyl oxygen
O ob Basal bridging oxygen
O oa Apical bridging oxygen
Si st Silicon in SiO2
Al ao Aluminium in the octahedral sheet
Al at Aluminium in Zeolites
Mg mgo Magnesium in the octahedral sheet
Ca cao Calcium in the octahedral sheet
Fe feo iron in the octahedral sheet
Li lio Lithium in the octahedral sheet
O obss bridging oxygen with double substitution
O obts bridging oxygen with tetrahedral substitution
O obos bridging oxygen with octahedral substitution
O ohs hydroxyl oxygen with substitution
Ca cah hydroxide calcium
Mg mgh hydroxide magnesium
Na Na Sodium ion
K K Potassium ion
Cs Cs Cs+ ion
Ca Ca Ca2+ ion
Ba Ba Ba2+ ion
Cl Cl Cl- ion

2.22.3.2.6. AlO_eam_coul.frc TaO_eam_coul.frc CeThUNpPuAmCmO_eam_coul.frc

These forcefields are known as the Streitz-Mintmire or charge-transfer ionic (CTIP) potentials [20] which combine EAM and Coulomb (charges described via Slater type orbitals instead of point charges) forcefields along with variable charge equilibration.

2.22.3.2.6.1. AlO_eam_coul.frc
Al Al  
O1 O1  
2.22.3.2.6.2. TaO_eam_coul.frc
Ta Ta  
O2 O2  
2.22.3.2.6.3. CeThUNpPuAmCmO_eam_coul.frc
Ce Ce  
Th Th  
U U  
Np Np  
Pu Pu  
Am Am  
Cm Cm  
O O  

2.22.3.2.7. comb3.frc Si-O_JCP2016-comb3.frc

The 3rd generation charge-optimized many-body (COMB3) [21] forcefields are improvements over the previous generations of COMB forcefields. COMB3 contains an advanced bond order term for describing complex chemical reactions (bond breaking and formation), Coulomb with charge density described with Slater-type orbitals, and variable charge equilibration (atomic charges automatically assigned based on atomic surroundings).

2.22.3.2.7.1. comb3.frc
Ti Ti Titanium
H H Hydrogen
C C Carbon
N N Nitrogen
O O Oxygen
Cu Cu Copper
Zn Zn Zinc
Zr Zr Zirconium
Si Si Silicon
Ti Ti Titanium
Al Al Aluminum
Ni Ni Nickel
Mo Mo Molybdenum
S S Sulfur
Pt Pt Platinum
Au Au Gold
2.22.3.2.7.2. Si-O_JCP2016-comb3.frc
O O Oxygen
Si Si Silicon

2.22.3.3. Semiconductors

Forcefields for semiconductor materials. These forcefields don’t require bonds.

2.22.3.3.1. StillingerWeber.frc ZnCdTeSeHgS_Zhou_2013_StillingerWeber.frc

Stilllinger-Weber forcefields that allow for the simulation of various crystalline and amorphous solids. This forcefield uses an explicit angular term to assess nearest neighbor coordination (to include three-body forces) based on the local environment of simulated atoms [22].

2.22.3.3.1.1. StillingerWeber.frc
Cd Cd cadmium
Ga Ga gallium
N N nitrogen
Si Si silicon
Te Te tellurium
2.22.3.3.1.2. ZnCdTeSeHgS_Zhou_2013_StillingerWeber.frc
Cd Cd cadmium
Zn Zn zinc
Te Te tellurium
Se Se selenium
Hg Hg mercury
S S sulfur

2.22.3.3.2. Tersoff.frc SiO2-Si_Munetoh_2007_Tersoff.frc

Tersoff forcefields that allow for the simulation of various crystalline and amorphous solids. This forcefield uses a bond order term to assess nearest neighbor coordination (to include three-body forces) based on the local environment of simulated atoms. [23]

2.22.3.3.2.1. Tersoff.frc
C C carbon
Ga Ga gallium
Ge Ge germanium
N N nitrogen
Si Si silicon, final parameters
Si Si(B) silicon, original parameters
Si Si(C) silicon, second set of parameters
O O oxygen atom
2.22.3.3.2.2. SiO2-Si_Munetoh_2007_Tersoff.frc
Si Si silicon, final parameters
O O oxygen atom

2.22.3.4. Metallic

The forcefields in this section don’t require bonds during atom type assignment and allow to study of metallic systems using the EAM (embedded atom model) description pioneered by Mike Baskes and others.

As noted above, the variability in local coordination inherent in inorganic systems (as opposed to organic systems) dictates that the creation of transferable forcefield descriptions is challenging for such systems. Hence, for each of the inorganic and metallic forcefield descriptions we recommend that the original references are consulted in order to assess the applicability of these descriptions to a particular system.

2.22.3.4.1. Zhou_2004.frc

This forcefield provides support for the following set of atoms and alloys composed of mixtures of these atoms. Zhou [24], with additions from Francis [25]

Ag Ag silver
Al Al aluminum
Au Au gold
Co Co cobalt
Cu Cu copper
Fe Fe iron
Mg Mg magnesium
Mo Mo molybdenum
Ni Ni nickel
Pb Pb lead
Pd Pd palladium
Pt Pt platinum
Ta Ta tantalum
Ti Ti titanium
W W tungsten
Zr Zr zirconium

2.22.3.4.2. EAM_Adams.frc

Li, Siegel, Adams, and Liu: [26]

Al Al aluminum
Au Au gold
Cu Cu copper
Ni Ni nickel
Pd Pd palladium
Pt Pt platinum
Ta Ta tantalum

2.22.3.4.3. Ni_EAM.frc

Mishin [27] , Ackland [28]

Ni Ni Nickel

2.22.3.4.4. ZrH_v4.frc

Mendelev [29]

H H hydrogen
Zr Zr zirconium

2.22.3.4.5. md-eam.frc

Updated pair interaction function

Zr Zr zirconium
Sn Sn tin
Cu Cu copper

2.22.3.4.6. FeNiCr_Bonny_2011.frc

EAM forcefield for alloys containing Fe, Ni, and Cr [30]

Fe Fe iron
Ni Ni nickel
Cr Cr chromium

2.22.3.4.7. AlCo_Mishin_2013.frc AlNi_Mishin_2009.frc AlTi_Mishin_2003.frc AlCu_Cai_1996.frc AlMg_Adams_1997.frc

EAM forcefields (eam/alloy format) for alloys containing Al/Co [31], Al/Ni [32], Al/Ti [33], Al/Cu [34], and Al/Mg [35].

Al Al aluminum
Co Co cobalt
Ni Ni nickel
Ti Ti titanium
Cu Cu copper
Mg Mg magnesium

2.22.3.4.8. AlSiMgCuFe_MEAM.frc AuSi_MEAM.frc CH_MEAM.frc Cu_MEAM.frc FeC_MEAM.frc FeTiC_MEAM.frc Ni_MEAM.frc SiC_MEAM.frc W_MEAM.frc…… MEAM.frc

Modified EAM (MEAM) forcefields include an additional angular term for a more accurate description of metals and alloys, including Al/Si/Mg/Cu/Fe [36], Au/Si [37], C/H [38], Fe/C [39], Fe/Ti/C [40], W [41], and Si/C, Cu, and Ni from the LAMMPS website. A generic MEAM.frc is also included to be used with custom MEAM forcefield parameter sets.

2.22.3.4.8.1. AlSiMgCuFe_MEAM.frc
Al Al aluminum
Si Si silicon
Mg Mg magnesium
Cu Cu copper
Fe Fe iron
2.22.3.4.8.2. AuSi_MEAM.frc
Au Au gold
Si Si silver
2.22.3.4.8.3. CH_MEAM.frc
C C carbon
H H hydrogen
2.22.3.4.8.4. FeC_MEAM.frc
Fe Fe iron
C C carbon
2.22.3.4.8.5. FeTiC_MEAM.frc
Fe Fe iron
Ti Ti titanium
C C carbon
2.22.3.4.8.6. W_MEAM.frc
W W tungsten
2.22.3.4.8.7. SiC_MEAM.frc
Si Si silicon
C C carbon
2.22.3.4.8.8. Ni_MEAM.frc
Ni Ni nickel
2.22.3.4.8.9. Cu_MEAM.frc
Cu Cu copper

2.22.3.5. NIST Interatomic Potentials Repository

Detailed descriptions are shown in the file selection dialog. These files are distributed with consent from Chandler A. Becker, the reviewer of this repository [42], http://www.ctcms.nist.gov/potentials.

2.22.3.6. ReaxFF Forcefields

Reactive Forcefields (ReaxFF) [43] is a family of well-established forcefields that simulate complex chemical reactions and charge transfer. It includes advanced bond terms over valence terms, shielded Coulomb, and variable charge equilibration.

2.22.3.6.1. AlLiSiO.frc

ReaxFF forcefield for Li in Si, SiOx nanowires [56]

Al Al aluminum
Li Li lithium
Si Si silicon
O O oxygen
H H hydrogen

2.22.3.6.2. AuOH.frc

ReaxFF forcefield for Au, AuOx and water [44] from LAMMPS potentials repository

Au Au gold
O O oxygen
H H hydrogen

2.22.3.6.3. BaZrYOH.frc

ReaxFF forcefield for H diffusion in Y-Doped BaZrO3 [57]

Ba Ba barium
C C carbon
H H hydrogen
O O oxygen
N N nitrogen
Y Y yttrium
Zr Zr zirconium

Warning

The following bond interactions are not included in this frc file:

  • C - Zr
  • C - Y
  • C - Ba
  • N - Zr
  • N - Y
  • N - Ba

2.22.3.6.4. CHO.frc

The well-established ReaxFF forcefield for combustion [45] simulations from LAMMPS potentials repository

C C carbon
O O oxygen
H H hydrogen

2.22.3.6.5. CHON.frc

The well-established ReaxFF forcefield for nitramines (RDX/HMX/TATB/PETN) [46] from LAMMPS potentials repository

C C carbon
O O oxygen
H H hydrogen
N N nitrogen

2.22.3.6.6. CHONSFPtClNi.frc

ReaxFF forcefield for fluorinated graphene [58]

C C carbon
O O oxygen
H H hydrogen
N N nitrogen
S S sulfur
F F fluorine
Cl Cl chlorine
Ni Ni nickel

Warning

The following bond interactions are not included in this frc file:

  • N - Ni
  • S - Cl
  • S - Ni
  • F - Cl
  • F - Ni
  • Cl - Ni

2.22.3.6.7. CHONSMoNi.frc

ReaxFF forcefield for combustion of coal char [59]

#elements C H O S Mo Ni N

C C carbon
O O oxygen
H H hydrogen
N N nitrogen
S S sulfur
Mo Mo molybdenum
Ni Ni nickel

Warning

The following bond interactions are not included in this frc file:

  • S - Ni
  • Mo - N
  • Ni - N

2.22.3.6.8. CeO.frc

Reactive force field for CeO2 [60]

Ce Ce cerium
O O oxygen

2.22.3.6.9. CuClOH.frc

ReaxFF forcefield for aqueous chloride and copper chloride [61]

Cu Cu copper
O O oxygen
H H hydrogen
Cl Cl chlorine

2.22.3.6.10. CuOH.frc

ReaxFF forcefield for Cu, copper oxide, copper hydroxide and water interactions [62]

Cu Cu copper
C C carbon
O O oxygen
H H hydrogen

Warning

The following bond interactions are not included in this frc file:

  • C - Cu

2.22.3.6.11. FeCrOS.frc

ReaxFF forcefield for Cr2O3 catalyst, butane, and Fe/Cr/O/S compounds [63]

C C carbon
O O oxygen
H H hydrogen
Cr Cr chromium
Cu Cu copper
Al Al aluminum
Fe Fe iron
Ni Ni nickel
S S sulfur

Warning

The following bond interactions are not included in this frc file:

  • C - Cu
  • Fe - Cu
  • Al - Cu
  • Ni - Cu
  • Ni - Cr
  • Cu - S
  • Cu - Cr

2.22.3.6.12. FeOCH.frc

ReaxFF forcefield for Fe/O/H (Fe, FeOx and water) with Cl [64]

C C carbon
O O oxygen
H H hydrogen
Fe Fe iron
Cl Cl chlorine

Warning

The following bond interactions are not included in this frc file:

  • C - Cl

2.22.3.6.13. HONB.frc

ReaxFF forcefield for Ammonia Borane [47] from LAMMPS potentials repository

B B boron
O O oxygen
H H hydrogen
N N nitrogen

2.22.3.6.14. LiC.frc

ReaxFF forcefield for Li/C [65]

C C carbon
O O oxygen
H H hydrogen
Li Li lithium

Warning

The following bond interactions are not included in this frc file:

  • O - C

2.22.3.6.15. LiMnO.frc

ReaxFF forcefield for LiMn2O4 and C/H/O/F [66]

C C carbon
O O oxygen
H H hydrogen
Li Li lithium
Mn Mn manganese
F F fluorine
P P phosphorus
Ni Ni nickel
Al Al aluminum

Warning

The following bond interactions are not included in this frc file:

  • C - Ni
  • C - Al
  • H - Ni
  • H - Al
  • O - Ni
  • O - Al
  • Mn - Ni
  • Mn - Al
  • Li - Ni
  • Li - Al
  • F - Ni
  • F - Al
  • P - Ni
  • P - Al
  • Ni - Ni
  • Ni - Al
  • Al - Al

2.22.3.6.16. LiPFCHO.frc

ReaxFF forcefield for LiPF6/poly(propylene glycol) diacrylate solid electrolyte [67]

C C carbon
O O oxygen
H H hydrogen
N N nitrogen
S S sulfur
Li Li lithium
Mo Mo molybdenum
F F fluorine
P P phosphorus
Ni Ni nickel
B B boron

Warning

The following bond interactions are not included in this frc file:

  • S - F
  • S - P
  • S - N
  • Mo - Li
  • Mo - B
  • Mo - F
  • Mo - P
  • Mo - N
  • Ni - Li
  • Ni - B
  • Ni - F
  • Ni - P
  • Ni - N
  • Li - B
  • B - P
  • B - N
  • P - N

2.22.3.6.17. LiSCFO.frc

ReaxFF forcefield for LiS and Li/SWCNT with Teflon [68]

C C carbon
O O oxygen
H H hydrogen
N N nitrogen
S S sulfur
Li Li lithium
Mo Mo molybdenum
F F fluorine
P P phosphorus
Ni Ni nickel
B B boron

Warning

The following bond interactions are not included in this frc file:

  • S - F
  • S - P
  • S - N
  • Mo - Li
  • Mo - B
  • Mo - F
  • Mo - P
  • Mo - N
  • Ni - Li
  • Ni - B
  • Ni - F
  • Ni - P
  • Ni - N
  • Li - B
  • B - P
  • B - N
  • P - N

2.22.3.6.18. LiSiCHOF.frc

ReaxFF forcefield for Si-based anode in LiB; contains parameters for C/H/O, Li2CO3, Li2O, and LiF [69]

C C carbon
O O oxygen
H H hydrogen
Si Si silicon
Li Li lithium
F F fluorine

2.22.3.6.19. MoS2.frc

ReaxFF forcefield for MoS2 [70]

C C carbon
O O oxygen
H H hydrogen
S S sulfur
Mo Mo molybdenum
Ni Ni nickel

Warning

The following bond interactions are not included in this frc file:

  • S - Ni

2.22.3.6.20. PdOCH.frc

ReaxFF forcefield for Pd nanoparticle catalysis with C/H/O [71]

C C carbon
O O oxygen
H H hydrogen
Pd Pd palladium

2.22.3.6.21. PtCH.frc

ReaxFF forcefield for Pt interacting with hydrocarbons and carbon platelets [72]

C C carbon
H H hydrogen
Pt Pt platinum

2.22.3.6.22. PtNiCHO.frc

ReaxFF forcefield for Pt-Ni Alloy Catalyst with C/H/O [73]

C C carbon
O O oxygen
H H hydrogen
Ni Ni nickel
Pt Pt platinum

2.22.3.6.23. PtO.frc

ReaxFF forcefield for Pt/O [74]

Pt Pt platinum
O O oxygen

2.22.3.6.24. TiOH.frc

ReaxFF forcefield for TiO2 and water interactions. Part of water branch [75]

C C carbon
O O oxygen
H H hydrogen
N N nitrogen
S S sulfur
Ti Ti titanium
Mg Mg magnesium
F F fluorine
P P phosphorus
Na Na sodium
Cl Cl chlorine

Warning

The following bond interactions are not included in this frc file:

  • C - Mg
  • S - Mg
  • S - P
  • Mg - F
  • P - F
  • Na - F
  • Ti - F
  • Cl - F

2.22.3.6.25. VCHO.frc

ReaxFF forcefield for V, VOx and water [48] from LAMMPS potentials repository

V V vanadium
O O oxygen
H H hydrogen
C C carbon

2.22.3.6.26. ZnOH.frc

ReaxFF forcefield for Zn, ZnOx and water [49] from LAMMPS potentials repository

Zn Zn zinc
O O oxygen
H H hydrogen

2.22.3.6.27. clay_zeolite_water.frc

ReaxFF forcefield for Water in Smectite Clay-Zeolite Composites [76]

C C carbon
O O oxygen
H H hydrogen
Fe Fe iron
Cl Cl chlorine
Si Si silicon
Al Al aluminum
Ca Ca calcium

Warning

The following bond interactions are not included in this frc file:

  • C - Cl
  • C - Ca
  • Fe - Si
  • Fe - Al
  • Fe - Ca
  • Cl - Si
  • Cl - Al
  • Cl - Ca

2.22.3.6.28. epoxy.frc

ReaxFF forcefield for describing the reactive crosslinking of polymers [77]

C C carbon
O O oxygen
H H hydrogen
N N nitrogen
S S sulfur
Mg Mg magnesium
P p phosphorus
Na Na sodium
Cu Cu copper
Cl Cl chlorine

Warning

The following bond interactions are not included in this frc file:

  • C - Mg
  • S - Mg
  • S - P
  • S - Na
  • S - Cu
  • S - Cl
  • Mg - Cu
  • Mg - Cl
  • P - Cu
  • P - Cl
  • Na - Cu
  • Na - Cl

2.22.3.6.29. protein_water.frc

ReaxFF forcefield for biomolecules in solution [78]

C C carbon
O O oxygen
H H hydrogen
N N nitrogen
S S sulfur
Mg Mg magnesium
P p phosphorus
Na Na sodium
Cu Cu copper
Cl Cl chlorine

Warning

The following bond interactions are not included in this frc file:

  • C - Mg
  • S - Mg
  • S - P
  • S - Na
  • S - Cu
  • S - Cl
  • Mg - Cu
  • Mg - Cl
  • P - Cu
  • P - Cl
  • Na - Cu
  • Na - Cl

2.22.3.7. Mesoscale Forcefields

Mesoscale forcefields are forcefields for simulations on time and length scales larger than the atomistic scale. In mesoscale simulations multiple atoms are collectively described as beads. The forcefields contain parameters for the interaction of these beads. How many atoms are represented by a bead varies between mesoscale forcefields. It can be just three or four heavy atoms, an entire functional group or even a monomer for polymer simulations.

With mesoscale forcefields time steps in dynamics simulations can be extended to ten or twenty femtoseconds. Therefore, it becomes possible to run simulations for microseconds and on systems with extents close to micrometers.

2.22.3.7.1. Martini.frc

Mesoscale forcefield for polymers and basic organic molecules [52]. The Martini forcefield was originally designed for the simulation of biomolecules. It has been parameterized in a systematic way, combining top-down and bottom-up strategies. The forcefield combines on average four heavy atoms and the attached hydrogens in one bead. Extensions to sugars, polymers, surfactants and nanoparticles are available. More information can be found on the Martini home page [54].

C1 C1 Apolar-Degree of polarity: 1 (low)
C2 C2 Apolar-Degree of polarity: 2
C3 C3 Apolar-Degree of polarity: 3
C4 C4 Apolar-Degree of polarity: 4
C5 C5 Apolar-Degree of polarity: 5 (high)
N N Nonpolar-Hydrogen bonding capabilities: donor/acceptor
N0 N0 Nonpolar-Hydrogen bonding capabilities: none
Na Na Nonpolar-Hydrogen bonding capabilities: acceptor
Nd Nd Nonpolar-Hydrogen bonding capabilities: donor
P1 P1 Polar-Degree of polarity: 1 (low)
P2 P2 Polar-Degree of polarity: 2
P3 P3 Polar-Degree of polarity: 3
P4 P4 Polar-Degree of polarity: 4
P5 P5 Polar-Degree of polarity: 5 (high)
Q Q Charged-Hydrogen bonding capabilities: donor/acceptor
Q0 Q0 Charged-Hydrogen bonding capabilities: none
Qa Qa Charged-Hydrogen bonding capabilities: acceptor
Qd Qd Charged-Hydrogen bonding capabilities: donor
SC1 SC1 Apolar for ring structures-Degree of polarity: 1 (low)
SC2 SC2 Apolar for ring structures-Degree of polarity: 2
SC3 SC3 Apolar for ring structures-Degree of polarity: 3
SC4 SC4 Apolar for ring structures-Degree of polarity: 4
SC5 SC5 Apolar for ring structures-Degree of polarity: 5 (high)
SN SN Nonpolar for ring structures-Hydrogen bonding capabilities: donor/acceptor
SN0 N0 Nonpolar for ring structures-Hydrogen bonding capabilities: none
SNa SNa Nonpolar for ring structures-Hydrogen bonding capabilities: acceptor
SNd SNd Nonpolar for ring structures-Hydrogen bonding capabilities: donor
SP1 SP1 Polar for ring structures-Degree of polarity: 1 (low)
SP2 SP2 Polar for ring structures-Degree of polarity: 2
SP3 SP3 Polar for ring structures-Degree of polarity: 3
SP4 SP4 Polar for ring structures-Degree of polarity: 4
SP5 SP5 Polar for ring structures-Degree of polarity: 5 (high)
SQ SQ Charged for ring structures-Hydrogen bonding capabilities: donor/acceptor
SQ0 SQ0 Charged for ring structures-Hydrogen bonding capabilities: none
SQa SQa Charged for ring structures-Hydrogen bonding capabilities: acceptor
SQd SQd Charged for ring structures-Hydrogen bonding capabilities: donor

2.22.3.7.2. Martini-3.0.frc

The Martini 3.0 mesoscale forcefield is a reparameterization of the Martini model to address certain deficiencies of the original parameterization [53]. It is used in a wide range of applications in structural biology, biophysics, biomedicine, nanotechnology and materials design. The reparameterization has focused on reducing interactions of molecules which were too strong in the original version resulting in more accurate simulations. In addition to the mapping of four heavy atoms to one bead in the original forcefield beads for three-to-one (small beads) and two-to-one (tiny beads) mappings have been introduced. Therefore, the number of bead types has increased significantly. More information can be found on the Martini home page [54].

P6 P6 Polar - degree of polarity: 6 (high)
P5 P5 Polar - degree of polarity: 5
P4 P4 Polar - degree of polarity: 4
P3 P3 Polar - degree of polarity: 3
P2 P2 Polar - degree of polarity: 2
P1 P1 Polar - degree of polarity: 1 (low)
N6 N6 Intermediate/non-polar - degree of polarity: 6 (high)
N5 N5 Intermediate/non-polar - degree of polarity: 5
N4 N4 Intermediate/non-polar - degree of polarity: 4
N3 N3 Intermediate/non-polar - degree of polarity: 3
N2 N2 Intermediate/non-polar - degree of polarity: 2
N1 N1 Intermediate/non-polar - degree of polarity: 1 (low)
C6 C6 Apolar - degree of polarity: 6 (high)
C5 C5 Apolar - degree of polarity: 5
C4 C4 Apolar - degree of polarity: 4
C3 C3 Apolar - degree of polarity: 3
C2 C2 Apolar - degree of polarity: 2
C1 C1 Apolar - degree of polarity: 1 (low)
X4 X4 Halo compound - polarity: 4 (high)
X3 X3 Halo compound - polarity: 3
X2 X2 Halo compound - polarity: 2
X1 X1 Halo compound - polarity: 1 (low)
P6d P6d Polar - degree of polarity: 6 (high), hydrogen bond donor
P5d P5d Polar - degree of polarity: 5, hydrogen bond donor
P4d P4d Polar - degree of polarity: 4, hydrogen bond donor
P3d P3d Polar - degree of polarity: 3, hydrogen bond donor
P2d P2d Polar - degree of polarity: 2, hydrogen bond donor
P1d P1d Polar - degree of polarity: 1 (low), hydrogen bond donor
N6d N6d Intermediate/non-polar - degree of polarity: 6 (high), hydrogen bond donor
N5d N5d Intermediate/non-polar - degree of polarity: 5, hydrogen bond donor
N4d N4d Intermediate/non-polar - degree of polarity: 4, hydrogen bond donor
N3d N3d Intermediate/non-polar - degree of polarity: 3, hydrogen bond donor
N2d N2d Intermediate/non-polar - degree of polarity: 2, hydrogen bond donor
N1d N1d Intermediate/non-polar - degree of polarity: 1 (low), hydrogen bond donor
P6a P6a Polar - degree of polarity: 6 (high), hydrogen bond acceptor
P5a P5a Polar - degree of polarity: 5, hydrogen bond acceptor
P4a P4a Polar - degree of polarity: 4, hydrogen bond acceptor
P3a P3a Polar - degree of polarity: 3, hydrogen bond acceptor
P2a P2a Polar - degree of polarity: 2, hydrogen bond acceptor
P1a P1a Polar - degree of polarity: 1 (low), hydrogen bond acceptor
N6a N6a Intermediate/non-polar - degree of polarity: 6 (high), hydrogen bond acceptor
N5a N5a Intermediate/non-polar - degree of polarity: 5, hydrogen bond acceptor
N4a N4a Intermediate/non-polar - degree of polarity: 4, hydrogen bond acceptor
N3a N3a Intermediate/non-polar - degree of polarity: 3, hydrogen bond acceptor
N2a N2a Intermediate/non-polar - degree of polarity: 2, hydrogen bond acceptor
N1a N1a Intermediate/non-polar - degree of polarity: 1 (low), hydrogen bond acceptor
C6v C6v Apolar - degree of polarity: 6 (high), electron acceptor
C5v C5v Apolar - degree of polarity: 5, electron acceptor
C4v C4v Apolar - degree of polarity: 4, electron acceptor
C3v C3v Apolar - degree of polarity: 3, electron acceptor
C2v C2v Apolar - degree of polarity: 2, electron acceptor
C1v C1v Apolar - degree of polarity: 1 (low), electron acceptor
X4v X4v Halo compound - polarity: 4 (high), electron acceptor
X3v X3v Halo compound - polarity: 3, electron acceptor
X2v X2v Halo compound - polarity: 2, electron acceptor
X1v X1v Halo compound - polarity: 1 (low), electron acceptor
C6e C6e Apolar - degree of polarity: 6 (high), electron donor
C5e C5e Apolar - degree of polarity: 5, electron donor
C4e C4e Apolar - degree of polarity: 4, electron donor
C3e C3e Apolar - degree of polarity: 3, electron donor
C2e C2e Apolar - degree of polarity: 2, electron donor
C1e C1e Apolar - degree of polarity: 1 (low), electron donor
X3e X3e Halo compound - polarity: 3, electron donor
X4e X4e Halo compound - polarity: 4 (high), electron donor
X2e X2e Halo compound - polarity: 2, electron donor
X1e X1e Halo compound - polarity: 1 (low), electron donor
D D Divalent ion
Q5 Q5 Monovalent ion - hardness: 5 (high)
Q4 Q4 Monovalent ion - hardness: 4
Q3 Q3 Monovalent ion - hardness: 3
Q2 Q2 Monovalent ion - hardness: 2
Q1 Q1 Monovalent ion - hardness: 1 (low)
Q5p Q5p Monovalent ion - hardness: 5 (high), hydrogen bond donor
Q4p Q4p Monovalent ion - hardness: 4, hydrogen bond donor
Q3p Q3p Monovalent ion - hardness: 3, hydrogen bond donor
Q2p Q2p Monovalent ion - hardness: 2, hydrogen bond donor
Q1p Q1p Monovalent ion - hardness: 1 (low), hydrogen bond donor
Q5n Q5n Monovalent ion - hardness: 5 (high), hydrogen bond acceptor
Q4n Q4n Monovalent ion - hardness: 4, hydrogen bond acceptor
Q3n Q3n Monovalent ion - hardness: 3, hydrogen bond acceptor
Q2n Q2n Monovalent ion - hardness: 2, hydrogen bond acceptor
Q1n Q1n Monovalent ion - hardness: 1 (low), hydrogen bond acceptor
P6q P6q Polar - degree of polarity: 6 (high), partial charge
P5q P5q Polar - degree of polarity: 5, partial charge
P4q P4q Polar - degree of polarity: 4, partial charge
P3q P3q Polar - degree of polarity: 3, partial charge
P2q P2q Polar - degree of polarity: 2, partial charge
P1q P1q Polar - degree of polarity: 1 (low), partial charge
N6q N6q Intermediate/non-polar - degree of polarity: 6 (high), partial charge
N5q N5q Intermediate/non-polar - degree of polarity: 5, partial charge
N4q N4q Intermediate/non-polar - degree of polarity: 4, partial charge
N3q N3q Intermediate/non-polar - degree of polarity: 3, partial charge
N2q N2q Intermediate/non-polar - degree of polarity: 2, partial charge
N1q N1q Intermediate/non-polar - degree of polarity: 1 (low), partial charge
C6q C6q Apolar - degree of polarity: 6 (high), partial charge
C5q C5q Apolar - degree of polarity: 5, partial charge
C4q C4q Apolar - degree of polarity: 4, partial charge
C3q C3q Apolar - degree of polarity: 3, partial charge
C2q C2q Apolar - degree of polarity: 2, partial charge
C1q C1q Apolar - degree of polarity: 1 (low), partial charge
X4q X4q Halo compound - polarity: 4 (high), partial charge
X3q X3q Halo compound - polarity: 3, partial charge
X2q X2q Halo compound - polarity: 2, partial charge
X1q X1q Halo compound - polarity: 1 (low), partial charge
P6dq P6dq Polar - degree of polarity: 6 (high), hydrogen bond donor, partial charge
P5dq P5dq Polar - degree of polarity: 5, hydrogen bond donor, partial charge
P4dq P4dq Polar - degree of polarity: 4, hydrogen bond donor, partial charge
P3dq P3dq Polar - degree of polarity: 3, hydrogen bond donor, partial charge
P2dq P2dq Polar - degree of polarity: 2, hydrogen bond donor, partial charge
P1dq P1dq Polar - degree of polarity: 1 (low), hydrogen bond donor, partial charge
N6dq N6dq Intermediate/non-polar - degree of polarity: 6 (high), hydrogen bond donor, partial charge
N5dq N5dq Intermediate/non-polar - degree of polarity: 5, hydrogen bond donor, partial charge
N4dq N4dq Intermediate/non-polar - degree of polarity: 4, hydrogen bond donor, partial charge
N3dq N3dq Intermediate/non-polar - degree of polarity: 3, hydrogen bond donor, partial charge
N2dq N2dq Intermediate/non-polar - degree of polarity: 2, hydrogen bond donor, partial charge
N1dq N1dq Intermediate/non-polar - degree of polarity: 1 (low), hydrogen bond donor, partial charge
P6aq P6aq Polar - degree of polarity: 6 (high), hydrogen bond acceptor, partial charge
P5aq P5aq Polar - degree of polarity: 5, hydrogen bond acceptor, partial charge
P4aq P4aq Polar - degree of polarity: 4, hydrogen bond acceptor, partial charge
P3aq P3aq Polar - degree of polarity: 3, hydrogen bond acceptor, partial charge
P2aq P2aq Polar - degree of polarity: 2, hydrogen bond acceptor, partial charge
P1aq P1aq Polar - degree of polarity: 1 (low), hydrogen bond acceptor, partial charge
N6aq N6aq Intermediate/non-polar - degree of polarity: 6 (high), hydrogen bond acceptor, partial charge
N5aq N5aq Intermediate/non-polar - degree of polarity: 5, hydrogen bond acceptor, partial charge
N4aq N4aq Intermediate/non-polar - degree of polarity: 4, hydrogen bond acceptor, partial charge
N3aq N3aq Intermediate/non-polar - degree of polarity: 3, hydrogen bond acceptor, partial charge
N2aq N2aq Intermediate/non-polar - degree of polarity: 2, hydrogen bond acceptor, partial charge
N1aq N1aq Intermediate/non-polar - degree of polarity: 1 (low), hydrogen bond acceptor, partial charge
C6vq C6vq Apolar - degree of polarity: 6 (high), partial charge, electron acceptor
C5vq C5vq Apolar - degree of polarity: 5, partial charge, electron acceptor
C4vq C4vq Apolar - degree of polarity: 4, partial charge, electron acceptor
C3vq C3vq Apolar - degree of polarity: 3, partial charge, electron acceptor
C2vq C2vq Apolar - degree of polarity: 2, partial charge, electron acceptor
C1vq C1vq Apolar - degree of polarity: 1 (low), partial charge, electron acceptor
X4vq X4vq Halo compound - polarity: 4 (high), partial charge, electron acceptor
X3vq X3vq Halo compound - polarity: 3, partial charge, electron acceptor
X2vq X2vq Halo compound - polarity: 2, partial charge, electron acceptor
X1vq X1vq Halo compound - polarity: 1 (low), partial charge, electron acceptor
C6eq C6eq Apolar - degree of polarity: 6 (high), electron donor, partial charge
C5eq C5eq Apolar - degree of polarity: 5, electron donor, partial charge
C4eq C4eq Apolar - degree of polarity: 4, electron donor, partial charge
C3eq C3eq Apolar - degree of polarity: 3, electron donor, partial charge
C2eq C2eq Apolar - degree of polarity: 2, electron donor, partial charge
C1eq C1eq Apolar - degree of polarity: 1 (low), electron donor, partial charge
X4eq X4eq Halo compound - polarity: 4 (high), electron donor, partial charge
X3eq X3eq Halo compound - polarity: 3, electron donor, partial charge
X2eq X2eq Halo compound - polarity: 2, electron donor, partial charge
X1eq X1eq Halo compound - polarity: 1 (low), electron donor, partial charge
P6h P6h Polar - degree of polarity: 6 (high), high self-interaction
P5h P5h Polar - degree of polarity: 5, high self-interaction
P4h P4h Polar - degree of polarity: 4, high self-interaction
P3h P3h Polar - degree of polarity: 3, high self-interaction
P2h P2h Polar - degree of polarity: 2, high self-interaction
P1h P1h Polar - degree of polarity: 1 (low), high self-interaction
N6h N6h Intermediate/non-polar - degree of polarity: 6 (high), high self-interaction
N5h N5h Intermediate/non-polar - degree of polarity: 5, high self-interaction
N4h N4h Intermediate/non-polar - degree of polarity: 4, high self-interaction
N3h N3h Intermediate/non-polar - degree of polarity: 3, high self-interaction
N2h N2h Intermediate/non-polar - degree of polarity: 2, high self-interaction
N1h N1h Intermediate/non-polar - degree of polarity: 1 (low), high self-interaction
C6h C6h Apolar - degree of polarity: 6 (high), high self-interaction
C5h C5h Apolar - degree of polarity: 5, high self-interaction
C4h C4h Apolar - degree of polarity: 4, high self-interaction
C3h C3h Apolar - degree of polarity: 3, high self-interaction
C2h C2h Apolar - degree of polarity: 2, high self-interaction
C1h C1h Apolar - degree of polarity: 1 (low), high self-interaction
X4h X4h Halo compound - polarity: 4 (high), high self-interaction
X3h X3h Halo compound - polarity: 3, high self-interaction
X2h X2h Halo compound - polarity: 2, high self-interaction
X1h X1h Halo compound - polarity: 1 (low), high self-interaction
P6dh P6dh Polar - degree of polarity: 6 (high), hydrogen bond donor, high self-interaction
P5dh P5dh Polar - degree of polarity: 5, hydrogen bond donor, high self-interaction
P4dh P4dh Polar - degree of polarity: 4, hydrogen bond donor, high self-interaction
P3dh P3dh Polar - degree of polarity: 3, hydrogen bond donor, high self-interaction
P2dh P2dh Polar - degree of polarity: 2, hydrogen bond donor, high self-interaction
P1dh P1dh Polar - degree of polarity: 1 (low), hydrogen bond donor, high self-interaction
N6dh N6dh Intermediate/non-polar - degree of polarity: 6 (high), hydrogen bond donor, high self-interaction
N5dh N5dh Intermediate/non-polar - degree of polarity: 5, hydrogen bond donor, high self-interaction
N4dh N4dh Intermediate/non-polar - degree of polarity: 4, hydrogen bond donor, high self-interaction
N3dh N3dh Intermediate/non-polar - degree of polarity: 3, hydrogen bond donor, high self-interaction
N2dh N2dh Intermediate/non-polar - degree of polarity: 2, hydrogen bond donor, high self-interaction
N1dh N1dh Intermediate/non-polar - degree of polarity: 1 (low), hydrogen bond donor, high self-interaction
P6ah P6ah Polar - degree of polarity: 6 (high), hydrogen bond acceptor, high self-interaction
P5ah P5ah Polar - degree of polarity: 5, hydrogen bond acceptor, high self-interaction
P4ah P4ah Polar - degree of polarity: 4, hydrogen bond acceptor, high self-interaction
P3ah P3ah Polar - degree of polarity: 3, hydrogen bond acceptor, high self-interaction
P2ah P2ah Polar - degree of polarity: 2, hydrogen bond acceptor, high self-interaction
P1ah P1ah Polar - degree of polarity: 1 (low), hydrogen bond acceptor, high self-interaction
N6ah N6ah Intermediate/non-polar - degree of polarity: 6 (high), hydrogen bond acceptor, high self-interaction
N5ah N5ah Intermediate/non-polar - degree of polarity: 5, hydrogen bond acceptor, high self-interaction
N4ah N4ah Intermediate/non-polar - degree of polarity: 4, hydrogen bond acceptor, high self-interaction
N3ah N3ah Intermediate/non-polar - degree of polarity: 3, hydrogen bond acceptor, high self-interaction
N2ah N2ah Intermediate/non-polar - degree of polarity: 2, hydrogen bond acceptor, high self-interaction
N1ah N1ah Intermediate/non-polar - degree of polarity: 1 (low), hydrogen bond acceptor, high self-interaction
C6vh C6vh Apolar - degree of polarity: 6 (high), high self-interaction, electron acceptor
C5vh C5vh Apolar - degree of polarity: 5, high self-interaction, electron acceptor
C4vh C4vh Apolar - degree of polarity: 4, high self-interaction, electron acceptor
C3vh C3vh Apolar - degree of polarity: 3, high self-interaction, electron acceptor
C2vh C2vh Apolar - degree of polarity: 2, high self-interaction, electron acceptor
C1vh C1vh Apolar - degree of polarity: 1 (low), high self-interaction, electron acceptor
X4vh X4vh Halo compound - polarity: 4 (high), high self-interaction, electron acceptor
X3vh X3vh Halo compound - polarity: 3, high self-interaction, electron acceptor
X2vh X2vh Halo compound - polarity: 2, high self-interaction, electron acceptor
X1vh X1vh Halo compound - polarity: 1 (low), high self-interaction, electron acceptor
C6eh C6eh Apolar - degree of polarity: 6 (high), electron donor, high self-interaction
C5eh C5eh Apolar - degree of polarity: 5, electron donor, high self-interaction
C4eh C4eh Apolar - degree of polarity: 4, electron donor, high self-interaction
C3eh C3eh Apolar - degree of polarity: 3, electron donor, high self-interaction
C2eh C2eh Apolar - degree of polarity: 2, electron donor, high self-interaction
C1eh C1eh Apolar - degree of polarity: 1 (low), electron donor, high self-interaction
X4eh X4eh Halo compound - polarity: 4 (high), electron donor, high self-interaction
X3eh X3eh Halo compound - polarity: 3, electron donor, high self-interaction
X2eh X2eh Halo compound - polarity: 2, electron donor, high self-interaction
X1eh X1eh Halo compound - polarity: 1 (low), electron donor, high self-interaction
P6r P6r Polar - degree of polarity: 6 (high), reduced self-interaction
P5r P5r Polar - degree of polarity: 5, reduced self-interaction
P4r P4r Polar - degree of polarity: 4, reduced self-interaction
P3r P3r Polar - degree of polarity: 3, reduced self-interaction
P2r P2r Polar - degree of polarity: 2, reduced self-interaction
P1r P1r Polar - degree of polarity: 1 (low), reduced self-interaction
N6r N6r Intermediate/non-polar - degree of polarity: 6 (high), reduced self-interaction
N5r N5r Intermediate/non-polar - degree of polarity: 5, reduced self-interaction
N4r N4r Intermediate/non-polar - degree of polarity: 4, reduced self-interaction
N3r N3r Intermediate/non-polar - degree of polarity: 3, reduced self-interaction
N2r N2r Intermediate/non-polar - degree of polarity: 2, reduced self-interaction
N1r N1r Intermediate/non-polar - degree of polarity: 1 (low), reduced self-interaction
C6r C6r Apolar - degree of polarity: 6 (high), reduced self-interaction
C5r C5r Apolar - degree of polarity: 5, reduced self-interaction
C4r C4r Apolar - degree of polarity: 4, reduced self-interaction
C3r C3r Apolar - degree of polarity: 3, reduced self-interaction
C2r C2r Apolar - degree of polarity: 2, reduced self-interaction
C1r C1r Apolar - degree of polarity: 1 (low), reduced self-interaction
X4r X4r Halo compound - polarity: 4 (high), reduced self-interaction
X3r X3r Halo compound - polarity: 3, reduced self-interaction
X2r X2r Halo compound - polarity: 2, reduced self-interaction
X1r X1r Halo compound - polarity: 1 (low), reduced self-interaction
P6dr P6dr Polar - degree of polarity: 6 (high), hydrogen bond donor, reduced self-interaction
P5dr P5dr Polar - degree of polarity: 5, hydrogen bond donor, reduced self-interaction
P4dr P4dr Polar - degree of polarity: 4, hydrogen bond donor, reduced self-interaction
P3dr P3dr Polar - degree of polarity: 3, hydrogen bond donor, reduced self-interaction
P2dr P2dr Polar - degree of polarity: 2, hydrogen bond donor, reduced self-interaction
P1dr P1dr Polar - degree of polarity: 1 (low), hydrogen bond donor, reduced self-interaction
N6dr N6dr Intermediate/non-polar - degree of polarity: 6 (high), hydrogen bond donor, reduced self-interaction
N5dr N5dr Intermediate/non-polar - degree of polarity: 5, hydrogen bond donor, reduced self-interaction
N4dr N4dr Intermediate/non-polar - degree of polarity: 4, hydrogen bond donor, reduced self-interaction
N3dr N3dr Intermediate/non-polar - degree of polarity: 3, hydrogen bond donor, reduced self-interaction
N2dr N2dr Intermediate/non-polar - degree of polarity: 2, hydrogen bond donor, reduced self-interaction
N1dr N1dr Intermediate/non-polar - degree of polarity: 1 (low), hydrogen bond donor, reduced self-interaction
P6ar P6ar Polar - degree of polarity: 6 (high), hydrogen bond acceptor, reduced self-interaction
P5ar P5ar Polar - degree of polarity: 5, hydrogen bond acceptor, reduced self-interaction
P4ar P4ar Polar - degree of polarity: 4, hydrogen bond acceptor, reduced self-interaction
P3ar P3ar Polar - degree of polarity: 3, hydrogen bond acceptor, reduced self-interaction
P2ar P2ar Polar - degree of polarity: 2, hydrogen bond acceptor, reduced self-interaction
P1ar P1ar Polar - degree of polarity: 1 (low), hydrogen bond acceptor, reduced self-interaction
N6ar N6ar Intermediate/non-polar - degree of polarity: 6 (high), hydrogen bond acceptor, reduced self-interaction
N5ar N5ar Intermediate/non-polar - degree of polarity: 5, hydrogen bond acceptor, reduced self-interaction
N4ar N4ar Intermediate/non-polar - degree of polarity: 4, hydrogen bond acceptor, reduced self-interaction
N3ar N3ar Intermediate/non-polar - degree of polarity: 3, hydrogen bond acceptor, reduced self-interaction
N2ar N2ar Intermediate/non-polar - degree of polarity: 2, hydrogen bond acceptor, reduced self-interaction
N1ar N1ar Intermediate/non-polar - degree of polarity: 1 (low), hydrogen bond acceptor, reduced self-interaction
C6vr C6vr Apolar - degree of polarity: 6 (high), reduced self-interaction, electron acceptor
C5vr C5vr Apolar - degree of polarity: 5, reduced self-interaction, electron acceptor
C4vr C4vr Apolar - degree of polarity: 4, reduced self-interaction, electron acceptor
C3vr C3vr Apolar - degree of polarity: 3, reduced self-interaction, electron acceptor
C2vr C2vr Apolar - degree of polarity: 2, reduced self-interaction, electron acceptor
C1vr C1vr Apolar - degree of polarity: 1 (low), reduced self-interaction, electron acceptor
X4vr X4vr Halo compound - polarity: 4 (high), reduced self-interaction, electron acceptor
X3vr X3vr Halo compound - polarity: 3, reduced self-interaction, electron acceptor
X2vr X2vr Halo compound - polarity: 2, reduced self-interaction, electron acceptor
X1vr X1vr Halo compound - polarity: 1 (low), reduced self-interaction, electron acceptor
C6er C6er Apolar - degree of polarity: 6 (high), electron donor, reduced self-interaction
C5er C5er Apolar - degree of polarity: 5, electron donor, reduced self-interaction
C4er C4er Apolar - degree of polarity: 4, electron donor, reduced self-interaction
C3er C3er Apolar - degree of polarity: 3, electron donor, reduced self-interaction
C2er C2er Apolar - degree of polarity: 2, electron donor, reduced self-interaction
C1er C1er Apolar - degree of polarity: 1 (low), electron donor, reduced self-interaction
X4er X4er Halo compound - polarity: 4 (high), electron donor, reduced self-interaction
X3er X3er Halo compound - polarity: 3, electron donor, reduced self-interaction
X2er X2er Halo compound - polarity: 2, electron donor, reduced self-interaction
X1er X1er Halo compound - polarity: 1 (low), electron donor, reduced self-interaction
SP6 SP6 Polar - degree of polarity: 6 (high), small
SP5 SP5 Polar - degree of polarity: 5, small
SP4 SP4 Polar - degree of polarity: 4, small
SP3 SP3 Polar - degree of polarity: 3, small
SP2 SP2 Polar - degree of polarity: 2, small
SP1 SP1 Polar - degree of polarity: 1 (low), small
SN6 SN6 Intermediate/non-polar - degree of polarity: 6 (high), small
SN5 SN5 Intermediate/non-polar - degree of polarity: 5, small
SN4 SN4 Intermediate/non-polar - degree of polarity: 4, small
SN3 SN3 Intermediate/non-polar - degree of polarity: 3, small
SN2 SN2 Intermediate/non-polar - degree of polarity: 2, small
SN1 SN1 Intermediate/non-polar - degree of polarity: 1 (low), small
SC6 SC6 Apolar - degree of polarity: 6 (high), small
SC5 SC5 Apolar - degree of polarity: 5, small
SC4 SC4 Apolar - degree of polarity: 4, small
SC3 SC3 Apolar - degree of polarity: 3, small
SC2 SC2 Apolar - degree of polarity: 2, small
SC1 SC1 Apolar - degree of polarity: 1 (low), small
SX4 SX4 Halo compound - polarity: 4 (high), small
SX3 SX3 Halo compound - polarity: 3, small
SX2 SX2 Halo compound - polarity: 2, small
SX1 SX1 Halo compound - polarity: 1 (low), small
SP6d SP6d Polar - degree of polarity: 6 (high), hydrogen bond donor, small
SP5d SP5d Polar - degree of polarity: 5, hydrogen bond donor, small
SP4d SP4d Polar - degree of polarity: 4, hydrogen bond donor, small
SP3d SP3d Polar - degree of polarity: 3, hydrogen bond donor, small
SP2d SP2d Polar - degree of polarity: 2, hydrogen bond donor, small
SP1d SP1d Polar - degree of polarity: 1 (low), hydrogen bond donor, small
SN6d SN6d Intermediate/non-polar - degree of polarity: 6 (high), hydrogen bond donor, small
SN5d SN5d Intermediate/non-polar - degree of polarity: 5, hydrogen bond donor, small
SN4d SN4d Intermediate/non-polar - degree of polarity: 4, hydrogen bond donor, small
SN3d SN3d Intermediate/non-polar - degree of polarity: 3, hydrogen bond donor, small
SN2d SN2d Intermediate/non-polar - degree of polarity: 2, hydrogen bond donor, small
SN1d SN1d Intermediate/non-polar - degree of polarity: 1 (low), hydrogen bond donor, small
SP6a SP6a Polar - degree of polarity: 6 (high), hydrogen bond acceptor, small
SP5a SP5a Polar - degree of polarity: 5, hydrogen bond acceptor, small
SP4a SP4a Polar - degree of polarity: 4, hydrogen bond acceptor, small
SP3a SP3a Polar - degree of polarity: 3, hydrogen bond acceptor, small
SP2a SP2a Polar - degree of polarity: 2, hydrogen bond acceptor, small
SP1a SP1a Polar - degree of polarity: 1 (low), hydrogen bond acceptor, small
SN6a SN6a Intermediate/non-polar - degree of polarity: 6 (high), hydrogen bond acceptor, small
SN5a SN5a Intermediate/non-polar - degree of polarity: 5, hydrogen bond acceptor, small
SN4a SN4a Intermediate/non-polar - degree of polarity: 4, hydrogen bond acceptor, small
SN3a SN3a Intermediate/non-polar - degree of polarity: 3, hydrogen bond acceptor, small
SN2a SN2a Intermediate/non-polar - degree of polarity: 2, hydrogen bond acceptor, small
SN1a SN1a Intermediate/non-polar - degree of polarity: 1 (low), hydrogen bond acceptor, small
SC6v SC6v Apolar - degree of polarity: 6 (high), electron acceptor, small
SC5v SC5v Apolar - degree of polarity: 5, electron acceptor, small
SC4v SC4v Apolar - degree of polarity: 4, electron acceptor, small
SC3v SC3v Apolar - degree of polarity: 3, electron acceptor, small
SC2v SC2v Apolar - degree of polarity: 2, electron acceptor, small
SC1v SC1v Apolar - degree of polarity: 1 (low), electron acceptor, small
SX4v SX4v Halo compound - polarity: 4 (high), electron acceptor, small
SX3v SX3v Halo compound - polarity: 3, electron acceptor, small
SX2v SX2v Halo compound - polarity: 2, electron acceptor, small
SX1v SX1v Halo compound - polarity: 1 (low), electron acceptor, small
SC6e SC6e Apolar - degree of polarity: 6 (high), electron donor, small
SC5e SC5e Apolar - degree of polarity: 5, electron donor, small
SC4e SC4e Apolar - degree of polarity: 4, electron donor, small
SC3e SC3e Apolar - degree of polarity: 3, electron donor, small
SC2e SC2e Apolar - degree of polarity: 2, electron donor, small
SC1e SC1e Apolar - degree of polarity: 1 (low), electron donor, small
SX4e SX4e Halo compound - polarity: 4 (high), electron donor, small
SX3e SX3e Halo compound - polarity: 3, electron donor, small
SX2e SX2e Halo compound - polarity: 2, electron donor, small
SX1e SX1e Halo compound - polarity: 1 (low), electron donor, small
SD SD Divalent ion, small
SQ5 SQ5 Monovalent ion - hardness: 5 (high), small
SQ4 SQ4 Monovalent ion - hardness: 4, small
SQ3 SQ3 Monovalent ion - hardness: 3, small
SQ2 SQ2 Monovalent ion - hardness: 2, small
SQ1 SQ1 Monovalent ion - hardness: 1 (low), small
SQ5p SQ5p Monovalent ion - hardness: 5 (high), hydrogen bond donor, small
SQ4p SQ4p Monovalent ion - hardness: 4, hydrogen bond donor, small
SQ3p SQ3p Monovalent ion - hardness: 3, hydrogen bond donor, small
SQ2p SQ2p Monovalent ion - hardness: 2, hydrogen bond donor, small
SQ1p SQ1p Monovalent ion - hardness: 1 (low), hydrogen bond donor, small
SQ5n SQ5n Monovalent ion - hardness: 5 (high), hydrogen bond acceptor, small
SQ4n SQ4n Monovalent ion - hardness: 4, hydrogen bond acceptor, small
SQ3n SQ3n Monovalent ion - hardness: 3, hydrogen bond acceptor, small
SQ2n SQ2n Monovalent ion - hardness: 2, hydrogen bond acceptor, small
SQ1n SQ1n Monovalent ion - hardness: 1 (low), hydrogen bond acceptor, small
SP6q SP6q Polar - degree of polarity: 6 (high), partial charge, small
SP5q SP5q Polar - degree of polarity: 5, partial charge, small
SP4q SP4q Polar - degree of polarity: 4, partial charge, small
SP3q SP3q Polar - degree of polarity: 3, partial charge, small
SP2q SP2q Polar - degree of polarity: 2, partial charge, small
SP1q SP1q Polar - degree of polarity: 1 (low), partial charge, small
SN6q SN6q Intermediate/non-polar - degree of polarity: 6 (high), partial charge, small
SN5q SN5q Intermediate/non-polar - degree of polarity: 5, partial charge, small
SN4q SN4q Intermediate/non-polar - degree of polarity: 4, partial charge, small
SN3q SN3q Intermediate/non-polar - degree of polarity: 3, partial charge, small
SN2q SN2q Intermediate/non-polar - degree of polarity: 2, partial charge, small
SN1q SN1q Intermediate/non-polar - degree of polarity: 1 (low), partial charge, small
SC6q SC6q Apolar - degree of polarity: 6 (high), partial charge, small
SC5q SC5q Apolar - degree of polarity: 5, partial charge, small
SC4q SC4q Apolar - degree of polarity: 4, partial charge, small
SC3q SC3q Apolar - degree of polarity: 3, partial charge, small
SC2q SC2q Apolar - degree of polarity: 2, partial charge, small
SC1q SC1q Apolar - degree of polarity: 1 (low), partial charge, small
SX4q SX4q Halo compound - polarity: 4 (high), partial charge, small
SX3q SX3q Halo compound - polarity: 3, partial charge, small
SX2q SX2q Halo compound - polarity: 2, partial charge, small
SX1q SX1q Halo compound - polarity: 1 (low), partial charge, small
SP6dq SP6dq Polar - degree of polarity: 6 (high), hydrogen bond donor, partial charge, small
SP5dq SP5dq Polar - degree of polarity: 5, hydrogen bond donor, partial charge, small
SP4dq SP4dq Polar - degree of polarity: 4, hydrogen bond donor, partial charge, small
SP3dq SP3dq Polar - degree of polarity: 3, hydrogen bond donor, partial charge, small
SP2dq SP2dq Polar - degree of polarity: 2, hydrogen bond donor, partial charge, small
SP1dq SP1dq Polar - degree of polarity: 1 (low), hydrogen bond donor, partial charge, small
SN6dq SN6dq Intermediate/non-polar - degree of polarity: 6 (high), hydrogen bond donor, partial charge, small
SN5dq SN5dq Intermediate/non-polar - degree of polarity: 5, hydrogen bond donor, partial charge, small
SN4dq SN4dq Intermediate/non-polar - degree of polarity: 4, hydrogen bond donor, partial charge, small
SN3dq SN3dq Intermediate/non-polar - degree of polarity: 3, hydrogen bond donor, partial charge, small
SN2dq SN2dq Intermediate/non-polar - degree of polarity: 2, hydrogen bond donor, partial charge, small
SN1dq SN1dq Intermediate/non-polar - degree of polarity: 1 (low), hydrogen bond donor, partial charge, small
SP6aq SP6aq Polar - degree of polarity: 6 (high), hydrogen bond acceptor, partial charge, small
SP5aq SP5aq Polar - degree of polarity: 5, hydrogen bond acceptor, partial charge, small
SP4aq SP4aq Polar - degree of polarity: 4, hydrogen bond acceptor, partial charge, small
SP3aq SP3aq Polar - degree of polarity: 3, hydrogen bond acceptor, partial charge, small
SP2aq SP2aq Polar - degree of polarity: 2, hydrogen bond acceptor, partial charge, small
SP1aq SP1aq Polar - degree of polarity: 1 (low), hydrogen bond acceptor, partial charge, small
SN6aq SN6aq Intermediate/non-polar - degree of polarity: 6 (high), hydrogen bond acceptor, partial charge, small
SN5aq SN5aq Intermediate/non-polar - degree of polarity: 5, hydrogen bond acceptor, partial charge, small
SN4aq SN4aq Intermediate/non-polar - degree of polarity: 4, hydrogen bond acceptor, partial charge, small
SN3aq SN3aq Intermediate/non-polar - degree of polarity: 3, hydrogen bond acceptor, partial charge, small
SN2aq SN2aq Intermediate/non-polar - degree of polarity: 2, hydrogen bond acceptor, partial charge, small
SN1aq SN1aq Intermediate/non-polar - degree of polarity: 1 (low), hydrogen bond acceptor, partial charge, small
SC6vq SC6vq Apolar - degree of polarity: 6 (high), partial charge, electron acceptor, small
SC5vq SC5vq Apolar - degree of polarity: 5, partial charge, electron acceptor, small
SC4vq SC4vq Apolar - degree of polarity: 4, partial charge, electron acceptor, small
SC3vq SC3vq Apolar - degree of polarity: 3, partial charge, electron acceptor, small
SC2vq SC2vq Apolar - degree of polarity: 2, partial charge, electron acceptor, small
SC1vq SC1vq Apolar - degree of polarity: 1 (low), partial charge, electron acceptor, small
SX4vq SX4vq Halo compound - polarity: 4 (high), partial charge, electron acceptor, small
SX3vq SX3vq Halo compound - polarity: 3, partial charge, electron acceptor, small
SX2vq SX2vq Halo compound - polarity: 2, partial charge, electron acceptor, small
SX1vq SX1vq Halo compound - polarity: 1 (low), partial charge, electron acceptor, small
SC6eq SC6eq Apolar - degree of polarity: 6 (high), electron donor, partial charge, small
SC5eq SC5eq Apolar - degree of polarity: 5, electron donor, partial charge, small
SC4eq SC4eq Apolar - degree of polarity: 4, electron donor, partial charge, small
SC3eq SC3eq Apolar - degree of polarity: 3, electron donor, partial charge, small
SC2eq SC2eq Apolar - degree of polarity: 2, electron donor, partial charge, small
SC1eq SC1eq Apolar - degree of polarity: 1 (low), electron donor, partial charge, small
SX4eq SX4eq Halo compound - polarity: 4 (high), electron donor, partial charge, small
SX3eq SX3eq Halo compound - polarity: 3, electron donor, partial charge, small
SX2eq SX2eq Halo compound - polarity: 2, electron donor, partial charge, small
SX1eq SX1eq Halo compound - polarity: 1 (low), electron donor, partial charge, small
SP6h SP6h Polar - degree of polarity: 6 (high), high self-interaction, small
SP5h SP5h Polar - degree of polarity: 5, high self-interaction, small
SP4h SP4h Polar - degree of polarity: 4, high self-interaction, small
SP3h SP3h Polar - degree of polarity: 3, high self-interaction, small
SP2h SP2h Polar - degree of polarity: 2, high self-interaction, small
SP1h SP1h Polar - degree of polarity: 1 (low), high self-interaction, small
SN6h SN6h Intermediate/non-polar - degree of polarity: 6 (high), high self-interaction, small
SN5h SN5h Intermediate/non-polar - degree of polarity: 5, high self-interaction, small
SN4h SN4h Intermediate/non-polar - degree of polarity: 4, high self-interaction, small
SN3h SN3h Intermediate/non-polar - degree of polarity: 3, high self-interaction, small
SN2h SN2h Intermediate/non-polar - degree of polarity: 2, high self-interaction, small
SN1h SN1h Intermediate/non-polar - degree of polarity: 1 (low), high self-interaction, small
SC6h SC6h Apolar - degree of polarity: 6 (high), high self-interaction, small
SC5h SC5h Apolar - degree of polarity: 5, high self-interaction, small
SC4h SC4h Apolar - degree of polarity: 4, high self-interaction, small
SC3h SC3h Apolar - degree of polarity: 3, high self-interaction, small
SC2h SC2h Apolar - degree of polarity: 2, high self-interaction, small
SC1h SC1h Apolar - degree of polarity: 1 (low), high self-interaction, small
SX4h SX4h Halo compound - polarity: 4 (high), high self-interaction, small
SX3h SX3h Halo compound - polarity: 3, high self-interaction, small
SX2h SX2h Halo compound - polarity: 2, high self-interaction, small
SX1h SX1h Halo compound - polarity: 1 (low), high self-interaction, small
SP6dh SP6dh Polar - degree of polarity: 6 (high), hydrogen bond donor, high self-interaction, small
SP5dh SP5dh Polar - degree of polarity: 5, hydrogen bond donor, high self-interaction, small
SP4dh SP4dh Polar - degree of polarity: 4, hydrogen bond donor, high self-interaction, small
SP3dh SP3dh Polar - degree of polarity: 3, hydrogen bond donor, high self-interaction, small
SP2dh SP2dh Polar - degree of polarity: 2, hydrogen bond donor, high self-interaction, small
SP1dh SP1dh Polar - degree of polarity: 1 (low), hydrogen bond donor, high self-interaction, small
SN6dh SN6dh Intermediate/non-polar - degree of polarity: 6 (high), hydrogen bond donor, high self-interaction, small
SN5dh SN5dh Intermediate/non-polar - degree of polarity: 5, hydrogen bond donor, high self-interaction, small
SN4dh SN4dh Intermediate/non-polar - degree of polarity: 4, hydrogen bond donor, high self-interaction, small
SN3dh SN3dh Intermediate/non-polar - degree of polarity: 3, hydrogen bond donor, high self-interaction, small
SN2dh SN2dh Intermediate/non-polar - degree of polarity: 2, hydrogen bond donor, high self-interaction, small
SN1dh SN1dh Intermediate/non-polar - degree of polarity: 1 (low), hydrogen bond donor, high self-interaction, small
SP6ah SP6ah Polar - degree of polarity: 6 (high), hydrogen bond acceptor, high self-interaction, small
SP5ah SP5ah Polar - degree of polarity: 5, hydrogen bond acceptor, high self-interaction, small
SP4ah SP4ah Polar - degree of polarity: 4, hydrogen bond acceptor, high self-interaction, small
SP3ah SP3ah Polar - degree of polarity: 3, hydrogen bond acceptor, high self-interaction, small
SP2ah SP2ah Polar - degree of polarity: 2, hydrogen bond acceptor, high self-interaction, small
SP1ah SP1ah Polar - degree of polarity: 1 (low), hydrogen bond acceptor, high self-interaction, small
SN6ah SN6ah Intermediate/non-polar - degree of polarity: 6 (high), hydrogen bond acceptor, high self-interaction, small
SN5ah SN5ah Intermediate/non-polar - degree of polarity: 5, hydrogen bond acceptor, high self-interaction, small
SN4ah SN4ah Intermediate/non-polar - degree of polarity: 4, hydrogen bond acceptor, high self-interaction, small
SN3ah SN3ah Intermediate/non-polar - degree of polarity: 3, hydrogen bond acceptor, high self-interaction, small
SN2ah SN2ah Intermediate/non-polar - degree of polarity: 2, hydrogen bond acceptor, high self-interaction, small
SN1ah SN1ah Intermediate/non-polar - degree of polarity: 1 (low), hydrogen bond acceptor, high self-interaction, small
SC6vh SC6vh Apolar - degree of polarity: 6 (high), high self-interaction, electron acceptor, small
SC5vh SC5vh Apolar - degree of polarity: 5, high self-interaction, electron acceptor, small
SC4vh SC4vh Apolar - degree of polarity: 4, high self-interaction, electron acceptor, small
SC3vh SC3vh Apolar - degree of polarity: 3, high self-interaction, electron acceptor, small
SC2vh SC2vh Apolar - degree of polarity: 2, high self-interaction, electron acceptor, small
SC1vh SC1vh Apolar - degree of polarity: 1 (low), high self-interaction, electron acceptor, small
SX4vh SX4vh Halo compound - polarity: 4 (high), high self-interaction, electron acceptor, small
SX3vh SX3vh Halo compound - polarity: 3, high self-interaction, electron acceptor, small
SX2vh SX2vh Halo compound - polarity: 2, high self-interaction, electron acceptor, small
SX1vh SX1vh Halo compound - polarity: 1 (low), high self-interaction, electron acceptor, small
SC6eh SC6eh Apolar - degree of polarity: 6 (high), electron donor, high self-interaction, small
SC5eh SC5eh Apolar - degree of polarity: 5, electron donor, high self-interaction, small
SC4eh SC4eh Apolar - degree of polarity: 4, electron donor, high self-interaction, small
SC3eh SC3eh Apolar - degree of polarity: 3, electron donor, high self-interaction, small
SC2eh SC2eh Apolar - degree of polarity: 2, electron donor, high self-interaction, small
SC1eh SC1eh Apolar - degree of polarity: 1 (low), electron donor, high self-interaction, small
SX4eh SX4eh Halo compound - polarity: 4 (high), electron donor, high self-interaction, small
SX3eh SX3eh Halo compound - polarity: 3, electron donor, high self-interaction, small
SX2eh SX2eh Halo compound - polarity: 2, electron donor, high self-interaction, small
SX1eh SX1eh Halo compound - polarity: 1 (low), electron donor, high self-interaction, small
SP6r SP6r Polar - degree of polarity: 6 (high), reduced self-interaction, small
SP5r SP5r Polar - degree of polarity: 5, reduced self-interaction, small
SP4r SP4r Polar - degree of polarity: 4, reduced self-interaction, small
SP3r SP3r Polar - degree of polarity: 3, reduced self-interaction, small
SP2r SP2r Polar - degree of polarity: 2, reduced self-interaction, small
SP1r SP1r Polar - degree of polarity: 1 (low), reduced self-interaction, small
SN6r SN6r Intermediate/non-polar - degree of polarity: 6 (high), reduced self-interaction, small
SN5r SN5r Intermediate/non-polar - degree of polarity: 5, reduced self-interaction, small
SN4r SN4r Intermediate/non-polar - degree of polarity: 4, reduced self-interaction, small
SN3r SN3r Intermediate/non-polar - degree of polarity: 3, reduced self-interaction, small
SN2r SN2r Intermediate/non-polar - degree of polarity: 2, reduced self-interaction, small
SN1r SN1r Intermediate/non-polar - degree of polarity: 1 (low), reduced self-interaction, small
SC6r SC6r Apolar - degree of polarity: 6 (high), reduced self-interaction, small
SC5r SC5r Apolar - degree of polarity: 5, reduced self-interaction, small
SC4r SC4r Apolar - degree of polarity: 4, reduced self-interaction, small
SC3r SC3r Apolar - degree of polarity: 3, reduced self-interaction, small
SC2r SC2r Apolar - degree of polarity: 2, reduced self-interaction, small
SC1r SC1r Apolar - degree of polarity: 1 (low), reduced self-interaction, small
SX4r SX4r Halo compound - polarity: 4 (high), reduced self-interaction, small
SX3r SX3r Halo compound - polarity: 3, reduced self-interaction, small
SX2r SX2r Halo compound - polarity: 2, reduced self-interaction, small
SX1r SX1r Halo compound - polarity: 1 (low), reduced self-interaction, small
SP6dr SP6dr Polar - degree of polarity: 6 (high), hydrogen bond donor, reduced self-interaction, small
SP5dr SP5dr Polar - degree of polarity: 5, hydrogen bond donor, reduced self-interaction, small
SP4dr SP4dr Polar - degree of polarity: 4, hydrogen bond donor, reduced self-interaction, small
SP3dr SP3dr Polar - degree of polarity: 3, hydrogen bond donor, reduced self-interaction, small
SP2dr SP2dr Polar - degree of polarity: 2, hydrogen bond donor, reduced self-interaction, small
SP1dr SP1dr Polar - degree of polarity: 1 (low), hydrogen bond donor, reduced self-interaction, small
SN6dr SN6dr Intermediate/non-polar - degree of polarity: 6 (high), hydrogen bond donor, reduced self-interaction, small
SN5dr SN5dr Intermediate/non-polar - degree of polarity: 5, hydrogen bond donor, reduced self-interaction, small
SN4dr SN4dr Intermediate/non-polar - degree of polarity: 4, hydrogen bond donor, reduced self-interaction, small
SN3dr SN3dr Intermediate/non-polar - degree of polarity: 3, hydrogen bond donor, reduced self-interaction, small
SN2dr SN2dr Intermediate/non-polar - degree of polarity: 2, hydrogen bond donor, reduced self-interaction, small
SN1dr SN1dr Intermediate/non-polar - degree of polarity: 1 (low), hydrogen bond donor, reduced self-interaction, small
SP6ar SP6ar Polar - degree of polarity: 6 (high), hydrogen bond acceptor, reduced self-interaction, small
SP5ar SP5ar Polar - degree of polarity: 5, hydrogen bond acceptor, reduced self-interaction, small
SP4ar SP4ar Polar - degree of polarity: 4, hydrogen bond acceptor, reduced self-interaction, small
SP3ar SP3ar Polar - degree of polarity: 3, hydrogen bond acceptor, reduced self-interaction, small
SP2ar SP2ar Polar - degree of polarity: 2, hydrogen bond acceptor, reduced self-interaction, small
SP1ar SP1ar Polar - degree of polarity: 1 (low), hydrogen bond acceptor, reduced self-interaction, small
SN6ar SN6ar Intermediate/non-polar - degree of polarity: 6 (high), hydrogen bond acceptor, reduced self-interaction, small
SN5ar SN5ar Intermediate/non-polar - degree of polarity: 5, hydrogen bond acceptor, reduced self-interaction, small
SN4ar SN4ar Intermediate/non-polar - degree of polarity: 4, hydrogen bond acceptor, reduced self-interaction, small
SN3ar SN3ar Intermediate/non-polar - degree of polarity: 3, hydrogen bond acceptor, reduced self-interaction, small
SN2ar SN2ar Intermediate/non-polar - degree of polarity: 2, hydrogen bond acceptor, reduced self-interaction, small
SN1ar SN1ar Intermediate/non-polar - degree of polarity: 1 (low), hydrogen bond acceptor, reduced self-interaction, small
SC6vr SC6vr Apolar - degree of polarity: 6 (high), reduced self-interaction, electron acceptor, small
SC5vr SC5vr Apolar - degree of polarity: 5, reduced self-interaction, electron acceptor, small
SC4vr SC4vr Apolar - degree of polarity: 4, reduced self-interaction, electron acceptor, small
SC3vr SC3vr Apolar - degree of polarity: 3, reduced self-interaction, electron acceptor, small
SC2vr SC2vr Apolar - degree of polarity: 2, reduced self-interaction, electron acceptor, small
SC1vr SC1vr Apolar - degree of polarity: 1 (low), reduced self-interaction, electron acceptor, small
SX4vr SX4vr Halo compound - polarity: 4 (high), reduced self-interaction, electron acceptor, small
SX3vr SX3vr Halo compound - polarity: 3, reduced self-interaction, electron acceptor, small
SX2vr SX2vr Halo compound - polarity: 2, reduced self-interaction, electron acceptor, small
SX1vr SX1vr Halo compound - polarity: 1 (low), reduced self-interaction, electron acceptor, small
SC6er SC6er Apolar - degree of polarity: 6 (high), electron donor, reduced self-interaction, small
SC5er SC5er Apolar - degree of polarity: 5, electron donor, reduced self-interaction, small
SC4er SC4er Apolar - degree of polarity: 4, electron donor, reduced self-interaction, small
SC3er SC3er Apolar - degree of polarity: 3, electron donor, reduced self-interaction, small
SC2er SC2er Apolar - degree of polarity: 2, electron donor, reduced self-interaction, small
SC1er SC1er Apolar - degree of polarity: 1 (low), electron donor, reduced self-interaction, small
SX4er SX4er Halo compound - polarity: 4 (high), electron donor, reduced self-interaction, small
SX3er SX3er Halo compound - polarity: 3, electron donor, reduced self-interaction, small
SX2er SX2er Halo compound - polarity: 2, electron donor, reduced self-interaction, small
SX1er SX1er Halo compound - polarity: 1 (low), electron donor, reduced self-interaction, small
TP6 TP6 Polar - degree of polarity: 6 (high), tiny
TP5 TP5 Polar - degree of polarity: 5, tiny
TP4 TP4 Polar - degree of polarity: 4, tiny
TP3 TP3 Polar - degree of polarity: 3, tiny
TP2 TP2 Polar - degree of polarity: 2, tiny
TP1 TP1 Polar - degree of polarity: 1 (low), tiny
TN6 TN6 Intermediate/non-polar - degree of polarity: 6 (high), tiny
TN5 TN5 Intermediate/non-polar - degree of polarity: 5, tiny
TN4 TN4 Intermediate/non-polar - degree of polarity: 4, tiny
TN3 TN3 Intermediate/non-polar - degree of polarity: 3, tiny
TN2 TN2 Intermediate/non-polar - degree of polarity: 2, tiny
TN1 TN1 Intermediate/non-polar - degree of polarity: 1 (low), tiny
TC6 TC6 Apolar - degree of polarity: 6 (high), tiny
TC5 TC5 Apolar - degree of polarity: 5, tiny
TC4 TC4 Apolar - degree of polarity: 4, tiny
TC3 TC3 Apolar - degree of polarity: 3, tiny
TC2 TC2 Apolar - degree of polarity: 2, tiny
TC1 TC1 Apolar - degree of polarity: 1 (low), tiny
TX4 TX4 Halo compound - polarity: 4 (high), tiny
TX3 TX3 Halo compound - polarity: 3, tiny
TX2 TX2 Halo compound - polarity: 2, tiny
TX1 TX1 Halo compound - polarity: 1 (low), tiny
TP6d TP6d Polar - degree of polarity: 6 (high), hydrogen bond donor, tiny
TP5d TP5d Polar - degree of polarity: 5, hydrogen bond donor, tiny
TP4d TP4d Polar - degree of polarity: 4, hydrogen bond donor, tiny
TP3d TP3d Polar - degree of polarity: 3, hydrogen bond donor, tiny
TP2d TP2d Polar - degree of polarity: 2, hydrogen bond donor, tiny
TP1d TP1d Polar - degree of polarity: 1 (low), hydrogen bond donor, tiny
TN6d TN6d Intermediate/non-polar - degree of polarity: 6 (high), hydrogen bond donor, tiny
TN5d TN5d Intermediate/non-polar - degree of polarity: 5, hydrogen bond donor, tiny
TN4d TN4d Intermediate/non-polar - degree of polarity: 4, hydrogen bond donor, tiny
TN3d TN3d Intermediate/non-polar - degree of polarity: 3, hydrogen bond donor, tiny
TN2d TN2d Intermediate/non-polar - degree of polarity: 2, hydrogen bond donor, tiny
TN1d TN1d Intermediate/non-polar - degree of polarity: 1 (low), hydrogen bond donor, tiny
TP6a TP6a Polar - degree of polarity: 6 (high), hydrogen bond acceptor, tiny
TP5a TP5a Polar - degree of polarity: 5, hydrogen bond acceptor, tiny
TP4a TP4a Polar - degree of polarity: 4, hydrogen bond acceptor, tiny
TP3a TP3a Polar - degree of polarity: 3, hydrogen bond acceptor, tiny
TP2a TP2a Polar - degree of polarity: 2, hydrogen bond acceptor, tiny
TP1a TP1a Polar - degree of polarity: 1 (low), hydrogen bond acceptor, tiny
TN6a TN6a Intermediate/non-polar - degree of polarity: 6 (high), hydrogen bond acceptor, tiny
TN5a TN5a Intermediate/non-polar - degree of polarity: 5, hydrogen bond acceptor, tiny
TN4a TN4a Intermediate/non-polar - degree of polarity: 4, hydrogen bond acceptor, tiny
TN3a TN3a Intermediate/non-polar - degree of polarity: 3, hydrogen bond acceptor, tiny
TN2a TN2a Intermediate/non-polar - degree of polarity: 2, hydrogen bond acceptor, tiny
TN1a TN1a Intermediate/non-polar - degree of polarity: 1 (low), hydrogen bond acceptor, tiny
TC6v TC6v Apolar - degree of polarity: 6 (high), electron acceptor, tiny
TC5v TC5v Apolar - degree of polarity: 5, electron acceptor, tiny
TC4v TC4v Apolar - degree of polarity: 4, electron acceptor, tiny
TC3v TC3v Apolar - degree of polarity: 3, electron acceptor, tiny
TC2v TC2v Apolar - degree of polarity: 2, electron acceptor, tiny
TC1v TC1v Apolar - degree of polarity: 1 (low), electron acceptor, tiny
TX4v TX4v Halo compound - polarity: 4 (high), electron acceptor, tiny
TX3v TX3v Halo compound - polarity: 3, electron acceptor, tiny
TX2v TX2v Halo compound - polarity: 2, electron acceptor, tiny
TX1v TX1v Halo compound - polarity: 1 (low), electron acceptor, tiny
TC6e TC6e Apolar - degree of polarity: 6 (high), electron donor, tiny
TC5e TC5e Apolar - degree of polarity: 5, electron donor, tiny
TC4e TC4e Apolar - degree of polarity: 4, electron donor, tiny
TC3e TC3e Apolar - degree of polarity: 3, electron donor, tiny
TC2e TC2e Apolar - degree of polarity: 2, electron donor, tiny
TC1e TC1e Apolar - degree of polarity: 1 (low), electron donor, tiny
TX4e TX4e Halo compound - polarity: 4 (high), electron donor, tiny
TX3e TX3e Halo compound - polarity: 3, electron donor, tiny
TX2e TX2e Halo compound - polarity: 2, electron donor, tiny
TX1e TX1e Halo compound - polarity: 1 (low), electron donor, tiny
TD TD Divalent ion, tiny
TQ5 TQ5 Monovalent ion - hardness: 5 (high), tiny
TQ4 TQ4 Monovalent ion - hardness: 4, tiny
TQ3 TQ3 Monovalent ion - hardness: 3, tiny
TQ2 TQ2 Monovalent ion - hardness: 2, tiny
TQ1 TQ1 Monovalent ion - hardness: 1 (low), tiny
TQ5p TQ5p Monovalent ion - hardness: 5 (high), hydrogen bond donor, tiny
TQ4p TQ4p Monovalent ion - hardness: 4, hydrogen bond donor, tiny
TQ3p TQ3p Monovalent ion - hardness: 3, hydrogen bond donor, tiny
TQ2p TQ2p Monovalent ion - hardness: 2, hydrogen bond donor, tiny
TQ1p TQ1p Monovalent ion - hardness: 1 (low), hydrogen bond donor, tiny
TQ5n TQ5n Monovalent ion - hardness: 5 (high), hydrogen bond acceptor, tiny
TQ4n TQ4n Monovalent ion - hardness: 4, hydrogen bond acceptor, tiny
TQ3n TQ3n Monovalent ion - hardness: 3, hydrogen bond acceptor, tiny
TQ2n TQ2n Monovalent ion - hardness: 2, hydrogen bond acceptor, tiny
TQ1n TQ1n Monovalent ion - hardness: 1 (low), hydrogen bond acceptor, tiny
TP6q TP6q Polar - degree of polarity: 6 (high), partial charge, tiny
TP5q TP5q Polar - degree of polarity: 5, partial charge, tiny
TP4q TP4q Polar - degree of polarity: 4, partial charge, tiny
TP3q TP3q Polar - degree of polarity: 3, partial charge, tiny
TP2q TP2q Polar - degree of polarity: 2, partial charge, tiny
TP1q TP1q Polar - degree of polarity: 1 (low), partial charge, tiny
TN6q TN6q Intermediate/non-polar - degree of polarity: 6 (high), partial charge, tiny
TN5q TN5q Intermediate/non-polar - degree of polarity: 5, partial charge, tiny
TN4q TN4q Intermediate/non-polar - degree of polarity: 4, partial charge, tiny
TN3q TN3q Intermediate/non-polar - degree of polarity: 3, partial charge, tiny
TN2q TN2q Intermediate/non-polar - degree of polarity: 2, partial charge, tiny
TN1q TN1q Intermediate/non-polar - degree of polarity: 1 (low), partial charge, tiny
TC6q TC6q Apolar - degree of polarity: 6 (high), partial charge, tiny
TC5q TC5q Apolar - degree of polarity: 5, partial charge, tiny
TC4q TC4q Apolar - degree of polarity: 4, partial charge, tiny
TC3q TC3q Apolar - degree of polarity: 3, partial charge, tiny
TC2q TC2q Apolar - degree of polarity: 2, partial charge, tiny
TC1q TC1q Apolar - degree of polarity: 1 (low), partial charge, tiny
TX4q TX4q Halo compound - polarity: 4 (high), partial charge, tiny
TX3q TX3q Halo compound - polarity: 3, partial charge, tiny
TX2q TX2q Halo compound - polarity: 2, partial charge, tiny
TX1q TX1q Halo compound - polarity: 1 (low), partial charge, tiny
TP6dq TP6dq Polar - degree of polarity: 6 (high), hydrogen bond donor, partial charge, tiny
TP5dq TP5dq Polar - degree of polarity: 5, hydrogen bond donor, partial charge, tiny
TP4dq TP4dq Polar - degree of polarity: 4, hydrogen bond donor, partial charge, tiny
TP3dq TP3dq Polar - degree of polarity: 3, hydrogen bond donor, partial charge, tiny
TP2dq TP2dq Polar - degree of polarity: 2, hydrogen bond donor, partial charge, tiny
TP1dq TP1dq Polar - degree of polarity: 1 (low), hydrogen bond donor, partial charge, tiny
TN6dq TN6dq Intermediate/non-polar - degree of polarity: 6 (high), hydrogen bond donor, partial charge, tiny
TN5dq TN5dq Intermediate/non-polar - degree of polarity: 5, hydrogen bond donor, partial charge, tiny
TN4dq TN4dq Intermediate/non-polar - degree of polarity: 4, hydrogen bond donor, partial charge, tiny
TN3dq TN3dq Intermediate/non-polar - degree of polarity: 3, hydrogen bond donor, partial charge, tiny
TN2dq TN2dq Intermediate/non-polar - degree of polarity: 2, hydrogen bond donor, partial charge, tiny
TN1dq TN1dq Intermediate/non-polar - degree of polarity: 1 (low), hydrogen bond donor, partial charge, tiny
TP6aq TP6aq Polar - degree of polarity: 6 (high), hydrogen bond acceptor, partial charge, tiny
TP5aq TP5aq Polar - degree of polarity: 5, hydrogen bond acceptor, partial charge, tiny
TP4aq TP4aq Polar - degree of polarity: 4, hydrogen bond acceptor, partial charge, tiny
TP3aq TP3aq Polar - degree of polarity: 3, hydrogen bond acceptor, partial charge, tiny
TP2aq TP2aq Polar - degree of polarity: 2, hydrogen bond acceptor, partial charge, tiny
TP1aq TP1aq Polar - degree of polarity: 1 (low), hydrogen bond acceptor, partial charge, tiny
TN6aq TN6aq Intermediate/non-polar - degree of polarity: 6 (high), hydrogen bond acceptor, partial charge, tiny
TN5aq TN5aq Intermediate/non-polar - degree of polarity: 5, hydrogen bond acceptor, partial charge, tiny
TN4aq TN4aq Intermediate/non-polar - degree of polarity: 4, hydrogen bond acceptor, partial charge, tiny
TN3aq TN3aq Intermediate/non-polar - degree of polarity: 3, hydrogen bond acceptor, partial charge, tiny
TN2aq TN2aq Intermediate/non-polar - degree of polarity: 2, hydrogen bond acceptor, partial charge, tiny
TN1aq TN1aq Intermediate/non-polar - degree of polarity: 1 (low), hydrogen bond acceptor, partial charge, tiny
TC6vq TC6vq Apolar - degree of polarity: 6 (high), partial charge, electron acceptor, tiny
TC5vq TC5vq Apolar - degree of polarity: 5, partial charge, electron acceptor, tiny
TC4vq TC4vq Apolar - degree of polarity: 4, partial charge, electron acceptor, tiny
TC3vq TC3vq Apolar - degree of polarity: 3, partial charge, electron acceptor, tiny
TC2vq TC2vq Apolar - degree of polarity: 2, partial charge, electron acceptor, tiny
TC1vq TC1vq Apolar - degree of polarity: 1 (low), partial charge, electron acceptor, tiny
TX4vq TX4vq Halo compound - polarity: 4 (high), partial charge, electron acceptor, tiny
TX3vq TX3vq Halo compound - polarity: 3, partial charge, electron acceptor, tiny
TX2vq TX2vq Halo compound - polarity: 2, partial charge, electron acceptor, tiny
TX1vq TX1vq Halo compound - polarity: 1 (low), partial charge, electron acceptor, tiny
TC6eq TC6eq Apolar - degree of polarity: 6 (high), electron donor, partial charge, tiny
TC5eq TC5eq Apolar - degree of polarity: 5, electron donor, partial charge, tiny
TC4eq TC4eq Apolar - degree of polarity: 4, electron donor, partial charge, tiny
TC3eq TC3eq Apolar - degree of polarity: 3, electron donor, partial charge, tiny
TC2eq TC2eq Apolar - degree of polarity: 2, electron donor, partial charge, tiny
TC1eq TC1eq Apolar - degree of polarity: 1 (low), electron donor, partial charge, tiny
TX4eq TX4eq Halo compound - polarity: 4 (high), electron donor, partial charge, tiny
TX3eq TX3eq Halo compound - polarity: 3, electron donor, partial charge, tiny
TX2eq TX2eq Halo compound - polarity: 2, electron donor, partial charge, tiny
TX1eq TX1eq Halo compound - polarity: 1 (low), electron donor, partial charge, tiny
TP6h TP6h Polar - degree of polarity: 6 (high), high self-interaction, tiny
TP5h TP5h Polar - degree of polarity: 5, high self-interaction, tiny
TP4h TP4h Polar - degree of polarity: 4, high self-interaction, tiny
TP3h TP3h Polar - degree of polarity: 3, high self-interaction, tiny
TP2h TP2h Polar - degree of polarity: 2, high self-interaction, tiny
TP1h TP1h Polar - degree of polarity: 1 (low), high self-interaction, tiny
TN6h TN6h Intermediate/non-polar - degree of polarity: 6 (high), high self-interaction, tiny
TN5h TN5h Intermediate/non-polar - degree of polarity: 5, high self-interaction, tiny
TN4h TN4h Intermediate/non-polar - degree of polarity: 4, high self-interaction, tiny
TN3h TN3h Intermediate/non-polar - degree of polarity: 3, high self-interaction, tiny
TN2h TN2h Intermediate/non-polar - degree of polarity: 2, high self-interaction, tiny
TN1h TN1h Intermediate/non-polar - degree of polarity: 1 (low), high self-interaction, tiny
TC6h TC6h Apolar - degree of polarity: 6 (high), high self-interaction, tiny
TC5h TC5h Apolar - degree of polarity: 5, high self-interaction, tiny
TC4h TC4h Apolar - degree of polarity: 4, high self-interaction, tiny
TC3h TC3h Apolar - degree of polarity: 3, high self-interaction, tiny
TC2h TC2h Apolar - degree of polarity: 2, high self-interaction, tiny
TC1h TC1h Apolar - degree of polarity: 1 (low), high self-interaction, tiny
TX4h TX4h Halo compound - polarity: 4 (high), high self-interaction, tiny
TX3h TX3h Halo compound - polarity: 3, high self-interaction, tiny
TX2h TX2h Halo compound - polarity: 2, high self-interaction, tiny
TX1h TX1h Halo compound - polarity: 1 (low), high self-interaction, tiny
TP6dh TP6dh Polar - degree of polarity: 6 (high), hydrogen bond donor, high self-interaction, tiny
TP5dh TP5dh Polar - degree of polarity: 5, hydrogen bond donor, high self-interaction, tiny
TP4dh TP4dh Polar - degree of polarity: 4, hydrogen bond donor, high self-interaction, tiny
TP3dh TP3dh Polar - degree of polarity: 3, hydrogen bond donor, high self-interaction, tiny
TP2dh TP2dh Polar - degree of polarity: 2, hydrogen bond donor, high self-interaction, tiny
TP1dh TP1dh Polar - degree of polarity: 1 (low), hydrogen bond donor, high self-interaction, tiny
TN6dh TN6dh Intermediate/non-polar - degree of polarity: 6 (high), hydrogen bond donor, high self-interaction, tiny
TN5dh TN5dh Intermediate/non-polar - degree of polarity: 5, hydrogen bond donor, high self-interaction, tiny
TN4dh TN4dh Intermediate/non-polar - degree of polarity: 4, hydrogen bond donor, high self-interaction, tiny
TN3dh TN3dh Intermediate/non-polar - degree of polarity: 3, hydrogen bond donor, high self-interaction, tiny
TN2dh TN2dh Intermediate/non-polar - degree of polarity: 2, hydrogen bond donor, high self-interaction, tiny
TN1dh TN1dh Intermediate/non-polar - degree of polarity: 1 (low), hydrogen bond donor, high self-interaction, tiny
TP6ah TP6ah Polar - degree of polarity: 6 (high), hydrogen bond acceptor, high self-interaction, tiny
TP5ah TP5ah Polar - degree of polarity: 5, hydrogen bond acceptor, high self-interaction, tiny
TP4ah TP4ah Polar - degree of polarity: 4, hydrogen bond acceptor, high self-interaction, tiny
TP3ah TP3ah Polar - degree of polarity: 3, hydrogen bond acceptor, high self-interaction, tiny
TP2ah TP2ah Polar - degree of polarity: 2, hydrogen bond acceptor, high self-interaction, tiny
TP1ah TP1ah Polar - degree of polarity: 1 (low), hydrogen bond acceptor, high self-interaction, tiny
TN6ah TN6ah Intermediate/non-polar - degree of polarity: 6 (high), hydrogen bond acceptor, high self-interaction, tiny
TN5ah TN5ah Intermediate/non-polar - degree of polarity: 5, hydrogen bond acceptor, high self-interaction, tiny
TN4ah TN4ah Intermediate/non-polar - degree of polarity: 4, hydrogen bond acceptor, high self-interaction, tiny
TN3ah TN3ah Intermediate/non-polar - degree of polarity: 3, hydrogen bond acceptor, high self-interaction, tiny
TN2ah TN2ah Intermediate/non-polar - degree of polarity: 2, hydrogen bond acceptor, high self-interaction, tiny
TN1ah TN1ah Intermediate/non-polar - degree of polarity: 1 (low), hydrogen bond acceptor, high self-interaction, tiny
TC6vh TC6vh Apolar - degree of polarity: 6 (high), high self-interaction, electron acceptor, tiny
TC5vh TC5vh Apolar - degree of polarity: 5, high self-interaction, electron acceptor, tiny
TC4vh TC4vh Apolar - degree of polarity: 4, high self-interaction, electron acceptor, tiny
TC3vh TC3vh Apolar - degree of polarity: 3, high self-interaction, electron acceptor, tiny
TC2vh TC2vh Apolar - degree of polarity: 2, high self-interaction, electron acceptor, tiny
TC1vh TC1vh Apolar - degree of polarity: 1 (low), high self-interaction, electron acceptor, tiny
TX4vh TX4vh Halo compound - polarity: 4 (high), high self-interaction, electron acceptor, tiny
TX3vh TX3vh Halo compound - polarity: 3, high self-interaction, electron acceptor, tiny
TX2vh TX2vh Halo compound - polarity: 2, high self-interaction, electron acceptor, tiny
TX1vh TX1vh Halo compound - polarity: 1 (low), high self-interaction, electron acceptor, tiny
TC6eh TC6eh Apolar - degree of polarity: 6 (high), electron donor, high self-interaction, tiny
TC5eh TC5eh Apolar - degree of polarity: 5, electron donor, high self-interaction, tiny
TC4eh TC4eh Apolar - degree of polarity: 4, electron donor, high self-interaction, tiny
TC3eh TC3eh Apolar - degree of polarity: 3, electron donor, high self-interaction, tiny
TC2eh TC2eh Apolar - degree of polarity: 2, electron donor, high self-interaction, tiny
TC1eh TC1eh Apolar - degree of polarity: 1 (low), electron donor, high self-interaction, tiny
TX4eh TX4eh Halo compound - polarity: 4 (high), electron donor, high self-interaction, tiny
TX3eh TX3eh Halo compound - polarity: 3, electron donor, high self-interaction, tiny
TX2eh TX2eh Halo compound - polarity: 2, electron donor, high self-interaction, tiny
TX1eh TX1eh Halo compound - polarity: 1 (low), electron donor, high self-interaction, tiny
TP6r TP6r Polar - degree of polarity: 6 (high), reduced self-interaction, tiny
TP5r TP5r Polar - degree of polarity: 5, reduced self-interaction, tiny
TP4r TP4r Polar - degree of polarity: 4, reduced self-interaction, tiny
TP3r TP3r Polar - degree of polarity: 3, reduced self-interaction, tiny
TP2r TP2r Polar - degree of polarity: 2, reduced self-interaction, tiny
TP1r TP1r Polar - degree of polarity: 1 (low), reduced self-interaction, tiny
TN6r TN6r Intermediate/non-polar - degree of polarity: 6 (high), reduced self-interaction, tiny
TN5r TN5r Intermediate/non-polar - degree of polarity: 5, reduced self-interaction, tiny
TN4r TN4r Intermediate/non-polar - degree of polarity: 4, reduced self-interaction, tiny
TN3r TN3r Intermediate/non-polar - degree of polarity: 3, reduced self-interaction, tiny
TN2r TN2r Intermediate/non-polar - degree of polarity: 2, reduced self-interaction, tiny
TN1r TN1r Intermediate/non-polar - degree of polarity: 1 (low), reduced self-interaction, tiny
TC6r TC6r Apolar - degree of polarity: 6 (high), reduced self-interaction, tiny
TC5r TC5r Apolar - degree of polarity: 5, reduced self-interaction, tiny
TC4r TC4r Apolar - degree of polarity: 4, reduced self-interaction, tiny
TC3r TC3r Apolar - degree of polarity: 3, reduced self-interaction, tiny
TC2r TC2r Apolar - degree of polarity: 2, reduced self-interaction, tiny
TC1r TC1r Apolar - degree of polarity: 1 (low), reduced self-interaction, tiny
TX4r TX4r Halo compound - polarity: 4 (high), reduced self-interaction, tiny
TX3r TX3r Halo compound - polarity: 3, reduced self-interaction, tiny
TX2r TX2r Halo compound - polarity: 2, reduced self-interaction, tiny
TX1r TX1r Halo compound - polarity: 1 (low), reduced self-interaction, tiny
TP6dr TP6dr Polar - degree of polarity: 6 (high), hydrogen bond donor, reduced self-interaction, tiny
TP5dr TP5dr Polar - degree of polarity: 5, hydrogen bond donor, reduced self-interaction, tiny
TP4dr TP4dr Polar - degree of polarity: 4, hydrogen bond donor, reduced self-interaction, tiny
TP3dr TP3dr Polar - degree of polarity: 3, hydrogen bond donor, reduced self-interaction, tiny
TP2dr TP2dr Polar - degree of polarity: 2, hydrogen bond donor, reduced self-interaction, tiny
TP1dr TP1dr Polar - degree of polarity: 1 (low), hydrogen bond donor, reduced self-interaction, tiny
TN6dr TN6dr Intermediate/non-polar - degree of polarity: 6 (high), hydrogen bond donor, reduced self-interaction, tiny
TN5dr TN5dr Intermediate/non-polar - degree of polarity: 5, hydrogen bond donor, reduced self-interaction, tiny
TN4dr TN4dr Intermediate/non-polar - degree of polarity: 4, hydrogen bond donor, reduced self-interaction, tiny
TN3dr TN3dr Intermediate/non-polar - degree of polarity: 3, hydrogen bond donor, reduced self-interaction, tiny
TN2dr TN2dr Intermediate/non-polar - degree of polarity: 2, hydrogen bond donor, reduced self-interaction, tiny
TN1dr TN1dr Intermediate/non-polar - degree of polarity: 1 (low), hydrogen bond donor, reduced self-interaction, tiny
TP6ar TP6ar Polar - degree of polarity: 6 (high), hydrogen bond acceptor, reduced self-interaction, tiny
TP5ar TP5ar Polar - degree of polarity: 5, hydrogen bond acceptor, reduced self-interaction, tiny
TP4ar TP4ar Polar - degree of polarity: 4, hydrogen bond acceptor, reduced self-interaction, tiny
TP3ar TP3ar Polar - degree of polarity: 3, hydrogen bond acceptor, reduced self-interaction, tiny
TP2ar TP2ar Polar - degree of polarity: 2, hydrogen bond acceptor, reduced self-interaction, tiny
TP1ar TP1ar Polar - degree of polarity: 1 (low), hydrogen bond acceptor, reduced self-interaction, tiny
TN6ar TN6ar Intermediate/non-polar - degree of polarity: 6 (high), hydrogen bond acceptor, reduced self-interaction, tiny
TN5ar TN5ar Intermediate/non-polar - degree of polarity: 5, hydrogen bond acceptor, reduced self-interaction, tiny
TN4ar TN4ar Intermediate/non-polar - degree of polarity: 4, hydrogen bond acceptor, reduced self-interaction, tiny
TN3ar TN3ar Intermediate/non-polar - degree of polarity: 3, hydrogen bond acceptor, reduced self-interaction, tiny
TN2ar TN2ar Intermediate/non-polar - degree of polarity: 2, hydrogen bond acceptor, reduced self-interaction, tiny
TN1ar TN1ar Intermediate/non-polar - degree of polarity: 1 (low), hydrogen bond acceptor, reduced self-interaction, tiny
TC6vr TC6vr Apolar - degree of polarity: 6 (high), reduced self-interaction, electron acceptor, tiny
TC5vr TC5vr Apolar - degree of polarity: 5, reduced self-interaction, electron acceptor, tiny
TC4vr TC4vr Apolar - degree of polarity: 4, reduced self-interaction, electron acceptor, tiny
TC3vr TC3vr Apolar - degree of polarity: 3, reduced self-interaction, electron acceptor, tiny
TC2vr TC2vr Apolar - degree of polarity: 2, reduced self-interaction, electron acceptor, tiny
TC1vr TC1vr Apolar - degree of polarity: 1 (low), reduced self-interaction, electron acceptor, tiny
TX4vr TX4vr Halo compound - polarity: 4 (high), reduced self-interaction, electron acceptor, tiny
TX3vr TX3vr Halo compound - polarity: 3, reduced self-interaction, electron acceptor, tiny
TX2vr TX2vr Halo compound - polarity: 2, reduced self-interaction, electron acceptor, tiny
TX1vr TX1vr Halo compound - polarity: 1 (low), reduced self-interaction, electron acceptor, tiny
TC6er TC6er Apolar - degree of polarity: 6 (high), electron donor, reduced self-interaction, tiny
TC5er TC5er Apolar - degree of polarity: 5, electron donor, reduced self-interaction, tiny
TC4er TC4er Apolar - degree of polarity: 4, electron donor, reduced self-interaction, tiny
TC3er TC3er Apolar - degree of polarity: 3, electron donor, reduced self-interaction, tiny
TC2er TC2er Apolar - degree of polarity: 2, electron donor, reduced self-interaction, tiny
TC1er TC1er Apolar - degree of polarity: 1 (low), electron donor, reduced self-interaction, tiny
TX4er TX4er Halo compound - polarity: 4 (high), electron donor, reduced self-interaction, tiny
TX3er TX3er Halo compound - polarity: 3, electron donor, reduced self-interaction, tiny
TX2er TX2er Halo compound - polarity: 2, electron donor, reduced self-interaction, tiny
TX1er TX1er Halo compound - polarity: 1 (low), electron donor, reduced self-interaction, tiny
W W Water
SW SW Water, small
TW TW Water, tiny

2.22.3.7.3. SPICA.frc

Mesoscale forcefield for polymers and basic organic molecules [55]. SPICA stands for Surface Property fItting Coarse grAined model. This forcefield has been designed to reproduce thermodynamic quantities, such as surface/interfacial tension and density, as well as distribution functions obtained from all-atom molecular simulations based on the CHARMM force field. The SPICA forcefield is suitable to simulate bio-molecular systems and soft matter.

C2T C2T -CH-(CH3)2
CLA CLA Cl- (H2O)2
CM CM -CH2-CH2-CH2-
CM2 CM2 -CH2-CH2- (tail)
CM2R CM2R CH2-CH2- (ring)
CM4 CM4 -CH2-C(-)H-CH2-CH3 branched tail group
CMB CMB -CH2-CH=CH- (ring B/C)
CMD CMD -CH=CH-CH2-
CMD2 CMD2 -HC=CH- (cis)
CMDB CMDB -CH2-C=CH- (ring A/B)
CMO CMO -CH2-CH2-CH2- (the same as CM)
CMR CMR -CH-CH2-CH2- (ring B/C)
CMR5 CMR5 -CH2-CH2-CH- (ring D)
CT CT CH3-CH2-CH2-
CT2 CT2 CH3-CH2-
CTB CTB same composition with CT2, but shorter bond length with CMT, CMY and CM4
CTBA CTBA -C-CH3 (ring A/B)
CTBB CTBB -C-CH3 (ring C/D)
EO EO -CH2-O-CH2-
EOT EOT CH3-O-CH2-
EST1 EST1 -CH2CO2- in the sn-2 chain
EST2 EST2 -H2CO2- in the sn-1 chain
GL GL -CH2CH-CH2-
GL2 GL2 -CH2-CH-
NC NC -CH2CH2-N-(CH3)3
NC4 NC4 (CH3)3N+CH2
NH NH -CH2CH2-NH3
OA OA HOCH2-
OAB OAB -CH-OH (ring A)
OAD OAD >CH-OH
PEP PEP -CO-NH-
PH PH -PO4-
PHE PHE -PO4- for PE headgroup
PHS PHS -PO4- (sphingomyelin)
SO4 SO4 SO4-
SOD SOD Na+ (H2O)3
W W three water molecules

2.22.3.8. Machine Learning Potentials (MLPs)

2.22.3.8.1. Cu-SNAP.frc

SNAP potential for Cu [79]

2.22.3.8.2. Cu_Zuo_JPCA2020.frc

SNAP potential for Cu [80]

2.22.3.8.3. Ge_Zuo_JPCA2020.frc

SNAP potential for Ge [80]

2.22.3.8.4. InP_JCPA2020.frc

SNAP potential for InP [80]

2.22.3.8.5. Li3N-SNAP.frc

SNAP potential for Li3N [82]

2.22.3.8.6. Li_Zuo_JPCA2020.frc

SNAP potential for Li [80]

2.22.3.8.7. Mo_Zuo_JPCA2020.frc

SNAP potential for Mo [80]

2.22.3.8.8. Ni_Zuo_JPCA2020.frc

SNAP potential for Ni [80]

2.22.3.8.9. Si_Zuo_JPCA2020.frc

SNAP potential for Si [80]

2.22.3.8.10. Mo-SNAP.frc

SNAP potential for Mo [83]

2.22.3.8.11. NbMoTaW-SNAP.frc

SNAP potential for Nb/Mo/Ta/W [84]

2.22.3.8.12. Ni-SNAP.frc

SNAP potential for Ni [88]

2.22.3.8.13. NiMo-SNAP.frc

SNAP potential for Ni/Mo [88]

2.22.3.8.14. Ta06A.frc

SNAP potential for Ta [85]

2.22.3.8.15. WBe_Wood_PRB2019.frc

SNAP potential for W/Be [86]

2.22.3.8.16. W_2940_2017_2.frc

SNAP potential for W [87]

2.22.4. The Materials Design Forcefield Format - FRC

The advantages of the .frc format are as follows:

  • automated atom type assignment using the templates section of the .frc file
  • wildcards
  • atom type equivalences for nonbonds, bonds, angles, torsions, etc.
  • versioning: each parameter has its own version, so updates do not remove older parameters but override them
  • includes: a user can modify a forcefield by including the original, adding parameters and, by using version numbers, override parameters in the original

The .frc format is much more compact and makes it easy to see and edit parameters. Wildcards are the ability to specify ‘*’ for an atom type. For example, the AUA forcefield specifies angles as C-CH2-C, where the terminal C can be almost any type of C atom, -CH3, -CH2-, -CH<, olefinic, ketone, etc. When you enumerate the permutations, it grows to be a very large list, which must be explicitly enumerated in e.g. GIBBS’ potparam.dat file.

With wildcards once specify one angle as *-CH2-*, where * matches any atom. More specific angles, like an alcohol *-C-O, including completely specific ones such as H-C-O take precedence in the obvious order. This also occurs in torsions, where typically the terminal atoms do not matter: *-CH2-CH2-*

For an example of the power of including forcefield files and version numbers, look at the oplsaa+.frc file, which includes the original oplsaa.frc, extensions published elsewhere (oplsaa-extended.frc), and adds some customs additions by Materials Design:

Include FF

!MD forcefield 1
#version oplsaa+.frc 1.0 12-Aug-2010
#define oplsaa+ default
!Ver Ref Function Label
!—- — ——————————— ——
1.0 1 atom_types oplsaa oplsaa-extended oplsaa+
1.0 1 equivalence oplsaa oplsaa-extended oplsaa+
1.0 1 quadratic_bond oplsaa oplsaa-extended oplsaa+
1.0 1 quadratic_angle oplsaa oplsaa-extended oplsaa+
1.0 1 torsion_opls oplsaa oplsaa-extended oplsaa+
1.0 1 wilson_out_of_plane oplsaa oplsaa-extended oplsaa+
1.0 1 nonbond(12-6) oplsaa oplsaa-extended oplsaa+
1.0 1 bond_increments oplsaa oplsaa-extended oplsaa+
1.0 1 templates oplsaa
#include oplsaa_extended.frc

The first section is a definition of the OPLSAA+ forcefield, listing the functional forms and the sections of the file(s) that contain the parameters. In this case the forcefield uses the ‘OPLSAA’ section (which will come from oplsaa.frc via an include in oplsaa-extended.frc) and the ‘oplsaa+’ section (which is in this file). Next it includes the entire extended OPLS forcefield.

Atom Types

#atom_types oplsaa+ 200


> Atom type definitions for oplsaa+
> Masses from OPLSAA publications

!Ver Ref Type Mass Element Connections Comment
!—- — —- ———- ————————————————
! 1.0 1 CT 12.011000 C 4 sp3 aliphatic carbon

#equivalence oplsaa+ 200
@columns nonbond bond angle torsion oop bond_increment

! Equivalences
!————————————————–
!Ver Ref Type NonB Bond Angle Torsion OOP BINCR
!—- — —- —- —- —– ——- —- —–
! 1.0 1 CT CT CT CT CT CT CT

#quadratic_bond oplsaa+ 200
> E = K2 * (R - R0)^2

!Ver Ref I J R0 K2
!—- — —- —- ——- ——–
! 1.0 1 CT CT 1.5290 268.0000

#quadratic_angle oplsaa+ 200
> E = K2 * (Theta - Theta0)^2

!Ver Ref I J K Theta0 K2
!—- — —- —- —- ——– ——-
! 1.0 1 CT CT CT 112.7000 58.3500

#torsion_opls oplsaa+ 200
> E = SUM(n=1,4) { [V(n)/2] * [ 1 - ((-1)^n)cos(n*Phi + Phi0(n)) ] }
> with ‘1-4’ interactions scaled by 0.5
@units V kcal/mol
@units Phi degree

!Ver Ref I J K L V1 Phi0 V2 Phi0 V3 Phi0 V4 Phi0
!——————————————————————————
! 1.0 1 CT CT CT CT 1.7400 0.0 -0.1570 0.0 0.2790 0.0 0.0000 0.0

#wilson_out_of_plane oplsaa+ 200
> E = K * (Chi - Chi0)^2

!Ver Ref I J K L K Chi0
!—- — —- —- —- —- ——- —-
! 1.1 4 CT CT HC HC 0.0 0.0

#nonbond(12-6) oplsaa+ 200
> E = 4.0*eps(ij) [(r0(ij)*/r(ij))**12 - (r0(ij)*/r(ij))**6]
> where r0(ij)* = sqrt((r0(i)*)*(r0(j)*))
> eps(ij) = sqrt(eps(i) * eps(j))
@combination geometric
@type r0-eps
@units Sigma Ang
@units Epsilon kcal/mol

!Ver Ref I r0 eps
!—- — —- ——— ———
! 1.0 1 CT 3.50000 0.06600

#bond_increments oplsaa+ 200

!Ver Ref I J DeltaIJ DeltaJI
!—- — —- —- ——- ——-
! 1.0 1 CT CT 0.0000 0.0000

#reference 1
Additional Materials Design OPLSAA forcefield parameters
@Author D. Rigby
@Date 12-Aug-2010
#end

This section adds a new atom type for sp3 aliphatic carbon, ‘CT’. Each section of the file has the name of the section optionally followed by an increment to version number, 200 in this case. This increment is added to the version numbers in the section, so the practical version number of the ‘CT’ atom type is 1.0+200 = 201.0. Assuming that the OPLSS/AA forcefield uses version numbers less than 200, the ‘CT’ atom type would override any ‘CT’ atom types in OPLSS/AA. This allows you to take similar forcefields and let one override the other without modifying all the version numbers.

The next section defines equivalences, which simply say that when looking for the bond parameters for ‘CAh1’use ‘CA’, but when looking for bond increase parameters, use a different value for ‘CAh1’, Thus we have a new atom type that is much like sp2 aromatic carbon, but the bond increments are different.

Equivalences

#equivalence oplsaa
@columns nonbond bond angle torsion oop bond_increment

! Equivalences
!————————————————–
!Ver Ref Type NonB Bond Angle Torsion OOP BINCR
!—- — —- —- —- —– ——- —- —–
1.0 1 Ar Ar Ar Ar Ar Ar Ar
1.1 4 C C C C C C C
1.0 1 CA CA CA CA CA CA CA
1.1 7 CAh1 CA CA CA CA CA CAh1

Having a higher version overrides the previous line, and now we can use specific bond increment parameters for our ‘CAh1’ atom type.

Bond Increments

#bond_increments oplsaa

!Ver Ref I J DeltaIJ DeltaJI
!—- — —- —- ——- ——-
1.0 1 CA CA 0.0000 0.0000
1.1 6 CA CZ1 0.0350 -0.0350
1.0 1 CA HA -0.1150 0.1150
1.1 9 CA OH5 0.1500 -0.1500
1.1 7 CAh1 CAh2 0.1460 -0.1460
1.1 7 CAh1 HA -0.0120 0.0120
1.1 7 CAh1 NC 0.3390 -0.3390

The last section of the example, the bond increment section, adds the bond parameters for our new ‘CAh1’ atom type. In addition, it adds or overrides some other bond parameters.

The final section concerns templates: It is by far the most complicated section, and unfortunately due to its nature cannot be versioned or added to. It must be taken as a whole unit because it specifies which atom type to assign to an atom in a structure, and hence is ‘aware’ of all the atom types in the forcefield and the relationship between them. Hence being monolithic.

If you need to modify the template section, copy the existing template section into the top level file and define this as the location of templates in the default section. Under normal circumstance you would inherit the template section from an included forcefield file and not touch it.

These extracts illustrate some of the important features. Each section defines how a local portion of the structure maps to an atom type. Each section is for an atom type and must contain the ‘template:’ line, which gives the topology.

Templates

#templates oplsaa

type: ?
! anything
template: (>*)
end_type

As usual, ‘*’ is a wild card.

Parentheses around the template indicate that there may be other bonds to the atom that are not contemplated in the template; square brackets indicate that the template includes all bonds, and that extra bonds are not allowed. So the first template matches anything.

The ‘*’ wildcard matches any element and the surrounding parentheses allow any number of bonds.

The atom type is ‘?’ which is our shorthand for an atom for which there are no parameters. The next template is also quite simple: it matches any argon atom, regardless of whether it has bonds to it or not. If we wanted an explicit match for just argon atoms, i.e. without any bonds, we would surround the template with square brackets instead of a parenthesis.

Template for Ar

type: Ar
! Argon atom
template: (>Ar)
end_type

For bonds we use ‘-‘ for single bonds, ‘=’ for double bonds, ‘:’ for aromatic bonds, and ‘#’ for triple bonds; ‘~’ matches any bond order, i.e. it is a wildcard.

Template for C in esters/acids

type:C
! Carbonyl carbon in carboxylate esters
template: (>C(-C)(-O(-C))(=O))
end_type

type:C
! Carbonyl carbon in carboxylic acids
template: (>C(=O)(-O(-H)))
end_type

Modifiers can narrow down the scope of wildcards: Allowed modifiers are hybridization, aromaticity, and elements:

Templates with wildcards

type:CA
! SP2 aromatic carbon
template:(>C(~*)(~*)(~*))
atom_test:1
hybridization: SP2
aromaticity:AROMATIC
end_test
end_type

type:CA
! This is used for aromatic carbons that fail the aromaticity test if
! the ring checker is unable to detect a ring with more than seven
! or eight sides. The NON_AROMATIC test is to eliminate the conflict
! with the above ‘CA’ definition.
template: [>C(-*)(:*)(:*)]
atom_test:1
hybridization:SP2
aromaticity:NON_AROMATIC
end_test
end_type

type:CAh1
! Aromatic carbon pyridine atom 2
template: (>C(:N))
end_type

type:CAh2
! Aromatic carbon pyridine atom 3
template: (>C(:C(:N)))
end_type

This template is quite specific for water. The square brackets both around the entire template and about the O and second H sees to that: there can be no other bonds anywhere.

Template with square brackets

type:HW
! TIP3P water hydrogen
template: [>H[-O[-H]]]
end_type

This template is less specific, but fits e.g. CO 2and CS 2. It would also fit e.g. Ar-C-Ar and other nonsensical structures.

Template with square brackets and wildcards

type:c2=
! Carbon in =C= (e.g. CO2, CS2)
template: [>C[~*][~*]]
end_type

This is a key issue in forcefields: they know what they do match, but not what they don’t!

With wildcards they tend to match many unintended things. So in the case of Ar-C-Ar, we would assign atom types just fine and (hopefully) still not be able to run because there would be missing Ar-C bond parameters and Ar-C-Ar angle parameters. On the other hand, if we had been lazy, and defined a set of generic bond parameters for ‘C-*’ and angle parameters for ‘*-C-*’ we would be off and running … garbage! It might be reasonable to have a catch-all angle term like ‘*-C-*’ since specific hybridization of the carbon atom (sp in this case) does roughly define the angle terms. But never a bond term like ‘C-*’! That is not reasonable since the bond length and strength depends on the second atom. And it is very dangerous, though the code will let you be foolish.

This brings us to more restraint use of wildcards: Here we see explicit tests that limit the power of the wildcards. The atom numbers are in the order the atoms appear in the templates, so the carbon of interest must be sp2; the two atoms other than oxygen that are bonded to it must be a C or H and an O or N. In other words this will match -C-C(=O)-OH, or H-C(=O)-OH, or -C-C(=O)-NH2 but not -C-C(=O)-C-. The modifiers for wildcards can be hybridization, which elements, and whether it is aromatic. At the moment, the code for recognizing hybridization and aromaticity is only partially complete.

Templates

type:c3’
! Carbonyl carbon [one polar substituent such as O,N]
! e.g. amide, acid and ester
template: (>C (~O) (~*) (~*))
atom_test:1
hybridization:sp2
end_test
atom_test:3
allowed_elements: C, H
end_test
atom_test:4
allowed_elements: O, N
end_test
end_type

The implementation in OPLS avoids the hybridization requirement and does not handle all cases, but goes through acids, esters, and, as shown amides:

Templates

type:C
! Carbonyl carbon in amides
template: (>C(-*)(=O)(-N(-*)(-*)))
atom_test:2
allowed_elements: C,H
end_test
atom_test:5
allowed_elements: C,H
end_test
atom_test:6
allowed_elements: C,H
end_test
end_type

Though not shown in this example, templates can match next nearest neighbors, etc. For example, the template for a carbon attached to an azide (-N3 group) looks like this:

Templates

type: c4z
! Carbon, sp3, bonded to -N3 (azides)
template: (>C(-N(~N(~N)))(-*)(-*)(-*))
atom_test:1
hybridization:SP3
end_test
end_type

The last section in the example is the precedence tree. An atom in a structure may match several templates, yielding different atom types. The precedence tree solves this ambiguity by providing a tree of atom types. The most specific match, i.e. the furthest from the trunk down a branch wins. The parentheses group the branches together but are admittedly rather hard to read.

Precedence tree

precedence:
(?
(Ar)
(C)
(CA (CAh1 (CQ) (CAh6)) (CAh2 (CAh5) (CAh7) (CAh8)) (CAh3 (CAh4)) (CR)
(CRh1)
(CS (CAh9) (CSh1(CV)) (CSh2 (CAh0) (CVh1)) (CU) (CUh1) (CWh1 (CWh3)
(CWh5)) (CWh2 (CWh4) (CWh6)) ) )
(CM)
(CO)
(CT (CT1) (CTEX) (CTfn) (CTf4) )
(CZ (CZ1) )
(F)
(H (HEX4) (HEX5) (HEX6) )
(HC (HA (HC2)) (HC1) (HC2) (HC3) (HC4) (HC5) (HC6) )
(He)
(HO (HW) )
(HS)
(Kr)
(N (N1) (N2) (N3))
(NA (NAh2) (NAh3))
(NB)
(NBh1)
(NBh2)
(NBh3)
(Ne)
(NC)
(NO)
(NT)
(NT0)
(NT2 (NTC4) )
(NT3)
(NZ)
(O)
(O1)
(O2)
(O3)
(O4)
(OH (OH2 (OH3) ) (OH4) (OH5) (OW) )
(ON)
(OS (OS1) )
(OW)
(S)
(SH)
(SH1)
(Xe)
)
end_precedence

Other groups such as AMBER do have some level of typing engines, but mostly the bio-organic community relies on the regularity of peptides, proteins and DNA to use systematic atom naming schemes and ‘template libraries’ to match the atom types. Thus a protein is built from peptide fragments that alcreated have the atom names and atom types assigned by hand. Since there are only twenty some amino acids, creating the fragment library is quite feasible. Proteins from the PDB also have systematic names for the atoms, so the template libraries match the atom types with the names. These are not, however, very general solutions.

[1]Huai Sun, Stephen J. Mumby, Jon R. Maple, and Arnold T. Hagler, “An Ab Initio CFF93 All-Atom Force Field for Polycarbonates,” Journal of the American Chemical Society 116, no. 7 (1994): 2978-2987.
[2]William L Jorgensen, David S Maxwell, and Julian Tirado-Rives, “Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids,” Journal of the American Chemical Society 118, no. 45 (January 1996): 11225-11236.
[3]MG Martin and IJ Siepmann, “Transferable Models for Phase Equilibria 1. United-Atom Description of N-Alkanes,” Journal of Physical Chemistry B 102 (1998): 2569.
[4]Ganesh Kamath, Feng Cao, and Jeffrey J Potoff, “An Improved Force Field for the Prediction of the Vapor-Liquid Equilibria for Carboxylic Acids,” Journal of Physical Chemistry B 108, no. 37 (September 2004): 14130-14136.
[5]John M Stubbs, Jeffrey J Potoff, and J Ilja Siepmann, “Transferable Potentials for Phase Equilibria. 6. United-Atom Description for Ethers, Glycols, Ketones, and Aldehydes,” Journal of Physical Chemistry B 108, no. 45 (November 2004): 17596-17605.
[6]Collin D Wick, John M Stubbs, Neeraj Rai, and J Ilja Siepmann, “Transferable Potentials for Phase Equilibria. 7. Primary, Secondary, and Tertiary Amines, Nitroalkanes and Nitrobenzene, Nitriles, Amides, Pyridine, and Pyrimidine,” Journal of Physical Chemistry B 109, no. 40 (October 2005): 18974-18982.
[7]Bin Chen, Jeffrey J Potoff, and J Ilja Siepmann, “Monte Carlo Calculations for Alcohols and Their Mixtures with Alkanes. Transferable Potentials for Phase Equilibria. 5. United-Atom Description of Primary, Secondary, and Tertiary Alcohols,” Journal of Physical Chemistry B 105, no. 15 (April 2001): 3093-3104.
[8]Collin D Wick, Marcus G Martin, and J Ilja Siepmann, “Transferable Potentials for Phase Equilibria. 4. United-Atom Description of Linear and Branched Alkenes and Alkylbenzenes,” Journal of Physical Chemistry B 104, no. 33 (August 2000): 8008-8016.
[9]MG Martin and IJ Siepmann, “Novel Configurational-Bias Monte Carlo Method for Branched Molecules. Transferable Potentials for Phase Equilibria. 2. United-Atoms Description of Branched Alkanes,” Journal of Physical Chemistry B 103 (1999): 4508.
[10]N Lubna, G Kamath, J J Potoff, N Rai, and J I Siepmann, “Transferable Potentials for Phase Equilibria. 8. United-Atom Description for Thiols, Sulfides, Disulfides, and Thiophene,” Journal of Physical Chemistry B 109, no. 50 (2005): 24100-24107.
[11]Katie A Maerzke, Nathan E Schultz, Richard B Ross, and J Ilja Siepmann, “TraPPE-UA Force Field for Acrylates and Monte Carlo Simulations for Their Mixtures with Alkanes and Alcohols,” Journal of Physical Chemistry B 113, no. 18 (May 7, 2009): 6415-6425.
[12]H Sun, “COMPASS: an Ab Initio Force-Field Optimized for Condensed-Phase -Overview with Details on Alkane and Benzene Compounds,” Journal of Physical Chemistry B 102, no. 38 (September 1998): 7338-7364.
[13]J\({\ddot{o}}\) rg-R diger Hill, Clive M Freeman, and Lalitha Subramanian, “Use of Force Fields in Materials Modeling,” in Reviews in Computational Chemistry, ed. by Kenny B Lipkowitz and Donald B Boyd, vol. 16, (Hoboken, NJ, USA: John Wiley & Sons, Inc., 2000), 141-216.
[14]J R Maple, M J Hwang, T P Stockfisch, U Dinur, M Waldman, et al., “Derivation of Class II Force Fields. I. Methodology and Quantum Force Field for the Alkyl Functional Group and Alkane Molecules,” Journal of Computational Chemistry 15, no. 2 (February 1994): 162-182; M J Hwang, T P Stockfisch, and A T Hagler, “Derivation of Class II Force Fields. 2. Derivation and Characterization of a Class II Force Field, CFF93, for the Alkyl Functional Group and Alkane Molecules,” Journal of the American Chemical Society 116, no. 6 (1994): 2515-2525.
[15]J R Maple, M J Hwang, T P Stockfisch, U Dinur, M Waldman, et al., “Derivation of Class II Force Fields. I. Methodology and Quantum Force Field for the Alkyl Functional Group and Alkane Molecules,” Journal of Computational Chemistry 15, no. 2 (February 1994): 162-182; M J Hwang, T P Stockfisch, and A T Hagler, “Derivation of Class II Force Fields. 2. Derivation and Characterization of a Class II Force Field, CFF93, for the Alkyl Functional Group and Alkane Molecules,” Journal of the American Chemical Society 116, no. 6 (1994): 2515-2525.
[16]S.M. Woodley, P.D. Battle, J D Gale, and C Richard A Catlow, “The Prediction of Inorganic Crystal Structures Using a Genetic Algorithm and Energy Minimisation,” Physical Chemistry Chemical Physics 1, no. 10 (1999): 2535-2542.
[17]Xin Xia, “Computational Modelling Study of Yttria-Stabilized Zirconia,” (University College London, 2010).
[18]B W H van Beest, G J Kramer, and R A van Santen, “Force Fields for Silicas and Aluminophosphates Based on Ab Initio Calculations,” Physical Review Letters 64, no. 16 (April 1990): 1955-1958.
[19]J\({\ddot{o}}\) rg-R diger Hill, Clive M Freeman, and Lalitha Subramanian, “Use of Force Fields in Materials Modeling,” in Reviews in Computational Chemistry, ed. by Kenny B Lipkowitz and Donald B Boyd, vol. 16, (Hoboken, NJ, USA: John Wiley & Sons, Inc., 2000), 141-216.
[20]F. H. Streitz and J. W. Mintmire, “Electrostatic potentials for metal-oxide surfaces and interfaces” Phys. Rev. B 50, 11996
[21]T. Liang, T.-R. Shan, Y.-T. Cheng, B. D. Devine, M. Noordhoek, Y. Li, Z. Lu, S. R. Phillpot, and S. B. Sinnott, Mat. Sci. & Eng: R 74, 255-279 (2013).
[22]Frank H Stillinger and Thomas A Weber, “Computer Simulation of Local Order in Condensed Phases of Silicon,” Physical Review B 31, no. 8 (1985): 5262-5271; A. B\({\grave{o}}\) r\({\grave{o}}\) and A. Serra, “On the Atomic Structures, Mobility and Interactions of Extended Defects in GaN: Dislocations, Tilt and Twin Boundaries,” Philosophical Magazine 86, no. 15 (2006): 2159-2192.
[23]J Tersoff, “New Empirical Approach for the Structure and Energy of Covalent Systems,” Physical Review B 37, no. 12 (1988): 6991-7000; J Tersoff, “Empirical Interatomic Potential for Silicon with Improved Elastic Properties,” Physical Review B 38, no. 14 (1988): 9902-9905; J Tersoff, “Modeling Solid-State Chemistry: Interatomic Potentials for Multicomponent Systems,” Physical Review B 39, no. 8 (1989): 5566-5568; J Tersoff, “Erratum: Modeling Solid-State Chemistry: Interatomic Potentials for Multicomponent Systems,” Physical Review B 41, no. 5 (1990): 3248-3248; “Modelling of Compound Semiconductors: Analytical Bond-Order Potential for Gallium, Nitrogen and Gallium Nitride,” Journal of Physics: Condensed Matter 15, no. 32 (2003): 5649.
[24]X Zhou, R Johnson, and H Wadley, “Misfit-Energy-Increasing Dislocations in Vapor-Deposited CoFe/NiFe Multilayers,” Physical Review B 69, no. 14 (April 2004).
[25]M F Francis, M N Neurock, X W Zhou, J J Quan, H N G Wadley, et al., “Atomic Assembly of Cu/Ta Multilayers: Surface Roughness, Grain Structure, Misfit Dislocations, and Amorphization,” Journal of Applied Physics 104, no. 3 (2008): 034310.
[26]Youhong Li, Donald J Siegel, James Adams, and Xiang-Yang Liu, “Embedded-Atom-Method Tantalum Potential Developed by the Force-Matching Method,” Physical Review B 67, no. 12 (2003).
[27]Yuri Mishin and Diana Farkas, “Atomistic Simulation of Point Defects and Diffusion in B2 NiAl Part1: Point Defect Energetics,” Philosophical Magazine A 75, no. 1 (1997): 169-185; Yuri Mishin and Diana Farkas, “Atomistic Simulation of Point Defects and Diffusion in B2 NiAl Part2: Diffusion Mechanisms,” Philosophical Magazine A 75, no. 1 (1997): 187-199.
[28]G J Ackland, G Tichy, V Vitek, and M W Finnis, “Simple N-Body Potentials for the Noble Metals and Nickel,” Philosophical Magazine A 56, no. 6 (December 1987): 735-756.
[29]M I Mendelev and G J Ackland, “Development of an Interatomic Potential for the Simulation of Phase Transformations in Zirconium,” Philosophical Magazine A 87, no. 5 (May 2007): 349-359.
[30]G. Bonny, D. Terentyev, R.C. Pasianot, S. Ponc\({\grave{o}}\) , and A. Bakaev, “Interatomic potential to study plasticity in stainless steels: the FeNiCr model alloy.” Modelling and simulation in materials science and engineering, 19, 085008 (2011)
[31]Purja Pun, G. P., Yamakov, V., and Mishin, Y. (2015). Interatomic potential for the ternary Ni-Al-Co system and application to atomistic modeling of the B2-L1 0 martensitic transformation. Modelling Simul. Mater. Sci. Eng., 23(6), 065006
[32]G.P. Purja Pun and Y. Mishin, “Development of an interatomic potential for the Ni-Al system,” Phil. Mag. 89, 3245 (2009).
[33]R.R. Zope and Y. Mishin, “Interatomic potentials for atomistic simulations of the Ti-Al system,” Phys. Rev. B 68, 024102 (2003)
[34]X.-Y. Liu, C.-L. Liu, and L.J. Borucki, “A new investigation of copper’s role in enhancing Al-Cu interconnect electromigration resistance from an atomistic view,” Acta Mat. 47, 3227-3231 (1999)
[35]X.-Y. Liu, P.P. Ohotnicky, J.B. Adams, C. Lane Rohrer, R.W. Hyland, Jr., “Anisotropic surface segregation in Al-Mg alloys,” Surf. Sci. 373, 357-370 (1997)
[36]B. Jelinek, S. Groh, M. Horstemeyer, J. Houze, S.G. Kim, G.J. Wagner, A. Moitra, and M.I. Baskes, “Modified embedded atom method potential for Al, Si, Mg, Cu, and Fe alloys,” Phys. Rev. B 85, 245102 (2012)
[37]J. Godet, C. Furgeaud, L. Pizzagalli, M. Demkowicz, “Uniform tensile elongation in Au-Si core-shell nanowires”, Extreme Mechanics Letters (2016)
[38]S. Nouranian, M.A. Tschopp, S.R. Gwaltney, M.I. Baskes, and M.F. Horstemeyer, “An interatomic potential for saturated hydrocarbons based on the modified embedded-atom method,” Physical Chemistry Chemical Physics 16, 6233 (2014).
[39]L.S.I. Liyanage, S.-G. Kim, J. Houze, S. Kim, M.A. Tschopp, M.I. Baskes, and M.F. Horstemeyer, “Structural, elastic, and thermal properties of cementite (Fe13C) calculated using a modified embedded atom method,” Phys. Rev. B 89, 094102 (2014)
[40]Kim, H.-K., Jung, W.-S., and Lee, B.-J. (2009). Modified embedded-atom method interatomic potentials for the Fe-Ti-C and Fe-Ti-N ternary systems. Acta Materialia, 57(11), 3140-3147.
[41]Lee, Baskes, Kim, Cho. Phys. Rev. B, 64, 184102 (2001)
[42]Chandler A Becker, Francesca Tavazza, Zachary T Trautt, and Robert A Buarque de Macedo, “Considerations for Choosing and Using Force Fields and Interatomic Potentials in Materials Science and Engineering,” Current Opinion in Solid State and Materials Science 17 (December 2013): 277-283.
[43]A.C.T. van Duin, S. Dasgupta, F. Lorant, and W. A. Goddard, ReaxFF: A reactive force field for hydrocarbons, Journal of Physical Chemistry A 105, 9396-9409 (2001); Chenoweth, A.C.T. van Duin, and W.A. Goddard, ReaxFF reactive force field for molecular dynamics simulations of hydrocarbon oxidation, Journal of Physical Chemistry A 112, 1040-1053 (2008)
[44]Keith, J. A. et al. Phys Rev B 2010, 81, 235404
[45]Chenoweth, A.C.T. van Duin, and W.A. Goddard, ReaxFF reactive force field for molecular dynamics simulations of hydrocarbon oxidation, Journal of Physical Chemistry A 112, 1040-1053 (2008)
[46]Strachan et al, Phys Rev Lett, 91, 098301 (2003)
[47]Weismiller, van Duin, Lee, Yetter, J Phys Chem A, 114, 5485-5492 (2010)
[48]Chenoweth et al, J Phys Chem C, 112, 14645-14654 (2008)
[49]mand, van Duin, Spangberg, Goddard and Hermansson, Surf Sci, 604, 741-752 (2010)
[50]Aryanpour, van Duin and Kubicki, J Phys Chem A, 114, 6298-6307 (2010)
[51]Singh, Phys Rev AB 87, 104114 (2013)
[52]Marrink, S. J., Risselada, H. J., Yefimov, S., Tieleman, D. P. and de Vries, A. H., J. Phys. Chem. B, 111, 7812-7824 (2007)
[53]“Martini 3: a general purpose force field for coarse-grained molecular dynamics” P. C. T. Souza, R. Alessandri, J. Barnoud, S. Thallmair, I. Faustino, F. Grünewald, I. Patmanidis, H. Abdizadeh, B. M. H. Bruininks, T. A. Wassenaar, P. C. Kroon, J. Melcr, V. Nieto, V. Corradi, H. M. Khan, J. Domański, M. Javanainen, H. Martinez-Seara, N. Reuter, R. B. Best, I. Vattulainen, L. Monticelli, X. Periole, D. P. Tieleman, A. H. de Vries and S. J. Marrink, Nature Methods 18, 382-388 (2021)
[54](1, 2) http://cgmartini.nl/index.php/martini
[55]http://www.spica-ff.org/
[56]“Stress effects on the initial lithiation of crystalline silicon nanowires: reactive molecular dynamics simulations using ReaxFF” Ostadhossein, Alireza and Cubuk, Ekin D. and Tritsaris, Georgios A. and Kaxiras, Efthimios and Zhang, Sulin and van Duin, Adri C. T. Phys. Chem. Chem. Phys., 2015,17, 3832-3840
[57]“ReaxFF Reactive Force Field for the Y-Doped BaZrO3 Proton Conductor with Applications to Diffusion Rates for Multigranular Systems” Adri C. T. van Duin, Boris V. Merinov, Sang Soo Han, Claudio O. Dorso, and William A. Goddard III J. Phys. Chem. A 2008, 112, 11414–11422
[58]Singh, Phys Rev AB 87, 104114 (2013)
[59]“Combustion of an Illinois No. 6 coal char simulated using an atomistic char representation and the ReaxFF reactive force field” Fidel Castro-Marcano, Amar M. Kamat, Michael F. Russo Jr., Adri C.T. van Duin, Jonathan P. Mathews Combustion and Flame 159 (2012) 1272–1285
[60]Broqvist et al. J. Phys. Chem. C 119(24), 13598-13609 (2015).
[61]Cu/O/H force field; van Duin et al., 2010 Cl parameters from Rahaman et al, 2010
[62]“Development and Validation of a ReaxFF Reactive Force Field for Cu Cation/Water Interactions and Copper Metal/Metal Oxide/Metal Hydroxide Condensed Phases” Adri C. T. van Duin, Vyacheslav S. Bryantsev, Mamadou S. Diallo, William A. Goddard, Obaidur Rahaman, Douglas J. Doren, David mand, and Kersti Hermansson J. Phys. Chem. A 2010, 114, 9507–9514
[63]“Development of a ReaxFF reactive force field for Fe/Cr/O/S and application to oxidation of butane over a pyrite-covered Cr2O3 catalyst.” Shin, Y.K., Kwak, H., Vasenkov, A., Sengupta, D. and van Duin, A.C.T., ACS Catalysis 5, 7226-7236.
[64]“Development of a Reactive Force Field for Iron-Oxyhydroxide Systems” Masoud Aryanpour, Adri C. T. van Duin, and James D. Kubicki, J. Phys. Chem. A 114, 21, 6298-6307
[65]“Reactive Force Field Study of Li/C Systems for Electrical Energy Storage” Muralikrishna Raju, P. Ganesh, R. C. Kent, and Adri C. T. van Duin, J. Chem. Theory Comput. 11, 5, 2156-2166
[66]“Chemical composition and formation mechanisms in the cathode-electrolyte interface layer of lithium manganese oxide batteries from reactive force field (ReaxFF) based molecular dynamics” Reddivari, S., Lastoskie, C., Wu, R. et al. Front. Energy (2017) 11: 365. https://doi.org/10.1007/s11708-017-0500-8
[67]“Salt concentration effects on mechanical properties of LiPF6/poly(propylene glycol) diacrylate solid electrolyte: Insights from reactive molecular dynamics simulations” Verners, O., Thijsse, B. J., van Duin, A. C. T., & Simone, A. Electrochimica Acta, 221, 115-123. DOI: 10.1016/j.electacta.2016.10.035
[68]“ReaxFF Reactive Force Field Simulations on the Influence of Teflon on Electrolyte Decomposition during Li/SWCNT Anode Discharge in Lithium-Sulfur Batteries” Md Mahbubul Islam, Vyacheslav S. Bryantsev, and Adri C. T. van Duin Journal of The Electrochemical Society, 161 (8) E3009-E3014 (2014)
[69]“Simulation Protocol for Prediction of a Solid-Electrolyte Interphase on the Silicon-based Anodes of a Lithium-Ion Battery: ReaxFF Reactive Force Field” Kang-Seop Yun, Sung Jin Pai, Byung Chul Yeo, Kwang-Ryeol Lee, Sun-Jae Kim, and Sang Soo Han, J. Phys. Chem. Lett. 8, 13, 2812-2818
[70]“ReaxFF Reactive Force-Field Study of Molybdenum Disulfide (MoS2)” Alireza Ostadhossein, Ali Rahnamoun, Yuanxi Wang, Peng Zhao, Sulin Zhang, Vincent H. Crespi, and Adri C. T. van Duin J. Phys. Chem. Lett. 2017, 8, 631-640
[71]“Determining in situ phases of a nanoparticle catalyst via grand canonical Monte Carlo simulations with the ReaxFF potential” Thomas P. Senftle, Adri C.T. van Duin, Michael J. Janik Catalysis Communications 52 (2014) 72-77
[72]“Molecular Dynamics Simulations of the Interactions between Platinum Clusters and Carbon Platelets” C.F. Sanz-Navarro, P.-O. Astrand, D. Chen, M. Eonning, A.C.T. van Duin, T. Jacob, and W.A. Goddard III J. Phys. Chem. A, 2008, 112 (7), pp 1392-1402
[73]“Development of a ReaxFF Reactive Force Field for the Pt-Ni Alloy Catalyst” Yun Kyung Shin, Lili Gai, Sumathy Raman, and Adri C. T. van Duin J. Phys. Chem. A 2016, 120, 8044-8055
[74]“Development of a ReaxFF potential for Pt-O systems describing the energetics and dynamics of Pt-oxide formation” Fantauzzi D, Bandlow J, Sabo L, Mueller JE, van Duin AC, Jacob T. Phys Chem Chem Phys. 2014 Nov 14;16(42):23118-33. doi: 10.1039/c4cp03111c.
[75]“Development of a ReaxFF Reactive Force Field for Titanium Dioxide/Water Systems” Sung-Yup Kim, Nitin Kumar, Petter Persson, Jorge Sofo, Adri C. T. van Duin, and James D. Kubicki Langmuir, 2013, 29 (25), pp 7838-7846
[76]“Dynamics of Confined Reactive Water in Smectite Clay-Zeolite Composites” Michael C. Pitman, and Adri C. T. van Duin, J. Am. Chem. Soc. 2012, 134, 3042-3053
[77]“Accelerated ReaxFF Simulations for Describing the Reactive Cross-Linking of Polymers” Aniruddh Vashisth, Chowdhury Ashraf, Weiwei Zhang, Charles E. Bakis, and Adri C. T. van Duin J. Phys. Chem. A 2018, 122, 6633-6642
[78]“Exploring the conformational and reactive dynamics of biomolecules in solution using an extended version of the glycine reactive force field” Susanna Monti, Alessandro Corozzi, Peter Fristrup, Kaushik L. Joshi, Yun Kyung Shin, Peter Oelschlaeger, Adri C. T. van Duin, and Vincenzo Barone Phys. Chem. Chem. Phys., 2013, 15, 15062
[79]X. Li, C. Hu, C. Chen, Z. Deng, J. Luo, & S.P. Ong (2018). “Quantum-Accurate Spectral Neighbor Analysis Potential Models for Ni-Mo Binary Alloys and FCC Metals.” arXiv:1806.04777
[80](1, 2, 3, 4, 5, 6, 7)
  1. Zuo, C. Chen, X, Li, Z. Deng, Y. Chen, J. Behler, G. Csányi, A. V. Shapeev, A. P. Thompson, M. A. Wood, S. P. Ong, “Performance and Cost Assessment of Machine Learning Interatomic Potentials” J. Phys. Chem. A 124, 4, 731-745 (2020)
[81]M.A. Cusentino, M. A. Wood, and A.P. Thompson, “Explicit Multi-element Extension of the Spectral Neighbor Analysis Potential for Chemically Complex Systems”, J. Phys. Chem. A, 124(26) 5456-5464 (2020). doi: 10.1021/acs.jpca.0c02450.
[82]
  1. Deng, C. Chen, X. Li & S.P. Ong (2019). “An Electrostatic Spectral Neighbor Analysis Potential (eSNAP) for Lithium Nitride.” arXiv:1901.08749
[83]Chen, C., Deng, Z., Tran, R., Tang, H., Chu, I. H., & Ong, S. P. (2017). Accurate force field for molybdenum by machine learning large materials data. Physical Review Materials, 1(4), 043603.
[84]
  1. Li, C. Chen, H. Zheng & S.P. Ong (2019). “Complex Strengthening Mechanisms in the NbMoTaW Multi-Principal Element Alloy with Machine Learning Potentials”, Cond. Mat Mat. Sci, https://arxiv.org/abs/1912.0178.
[85]Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
[86]M.A. Wood, M.A. Cusentino, B.D. Wirth, and A.P. Thompson, “Data-driven material models for atomistic simulation”, Physical Review B 99, 184305 (2019)
[87]Wood, M. A. and Thompson, A. P. “Quantum-Accurate Molecular Dynamics Potential for Tungsten” arXiv:1702.07042 [physics.comp-ph]
[88](1, 2)
  1. Li, C. Hu, C. Chen, Z. Deng, J. Luo, & S.P. Ong (2018). Quantum-Accurate Spectral Neighbor Analysis Potential Models for Ni-Mo Binary Alloys and FCC Metals. arXiv:1806.04777
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