Foce field schemes

In molecular simulations, FF parameters are usually derived by some empirical rules, either derived from some experimental observations or quantum mechanical calculations. Different research groups use different rules to obtain these parameters. Collectively, a set of rules that model a class of molecules is called a force field (FF) scheme.

DL_FIELD implements a wide range of FF schemes as shown below:

• CHARMM - For biomolecules including small drug molecules.

• AMBER - For biomolecules including small drug molecules..

• OPLS2005 - For biomolecules, general organic molecules and drug molecules.

• OPLS-DES - Deep eutectic solvents.

• OPLS CL&P - Organic cationic and anionic species for ionic liquids.

• OPLS AA/M - Protein molecules.

• PCFF - General organic molecules, organic polymers, Si-based structures.

• CVFF - General organic molecules.

• TraPPE-EH - Small organic molecules, for phase equilibria simulations.

• Dreiding - General FF for covalent molecules.

• Inorgnic - force fields for inorganic materials.

• CHARMM19 - United atom protein model.

• G54A7 - united atom Gromos FF.

• MISC FF - general purpose definable FF.

FF Scheme Structures

Each FF scheme (XX) consists of the following file components:

• Structure file (.sf), XX.sf.

• Parameter file (.par), XX.par.

• Miscellaneous supporting files for some FF schemes.

These files are located in the lib/ directory and they are all expressed in the same format for all FF schemes.

Some FF schemes are sub-divided for different types or classes of molecules. For instance, CHARMM force fields consist of schemes for amino acids (proteins), nuclei acids (DNA, RNA), carbohydrates and general organic molecules. In DL_FIELD, these sub divisions are considered to be independant FF schemes, although collectively they are compatible to one another.

An FF scheme must always be scpecified in the control file when running DL_FIELD. The program also allows multiple potential scenerios by specifying more than one different FF schemes. For more details, please see Multiple Potential Features.

Table below lists the available FF schemes with the corresponding scheme labels.

FF schemes	Labels	Example structures
CHARMM22 for proteins	CHARMM22_prot	amino acid residues, fitted molecules
CHARMM36 for proteins	CHARMM36_prot	amino acid residues, fitted molecules
CHARMM36 for nuclei acids	CHARMM36_nucl	DNA, RNA
CHARMM36 for lipids	CHARMM36_lipid	lipid molecules
CHARMM36 for carbohydrates	CHARMM36_carb	sugar molecules
CHARMM36 gneral force field	CHARMM36_cgenff	organic molecules, biomolecules
Amber including Glycam FF	AMBER	Amino acids, carbohydrates.
Amber general force field	AMBER16_gaff	Organic molecules.
OPLS_2005	OPLS2005	General organic molecules.
OPLS AA/M for proteins	OPLS_AAM	amino acid residues
OPLS CL&P	OPLS_CL_P	ionic liquids
OPLS for deep eutetic solvents	OPLS_DES	organic solvent molecules
DREIDING	DREIDING	General organic molecules
Polymer consistent force field	PCFF	General molecules, organosilica
Consistent valence force field	CVFF	General organic molecules
COMPASS	COMPASS	General organic molecules
Transferable potentials for phase equilibria	TRAPPE_EH	General organic molecules, small aromatics
Inorganic FF for binary oxides	INORGANIC_binary_oxide	Mineral oxides, MO2, MO
Inorganic FF for ternary oxides	INORGANIC_ternary_oxide	Minerals, MXO
Inorganic FF for binary halides	INORGANIC_binary_halide	MX, X=F, Cl, Br, I
Inorganic FF for glass	INORGANIC_glass	alumino-silicate, phosphate glass, etc
Inorganic FF for clay	INORGANIC_clay	Clay minerals, CLAYFF.
Inorganic FF zeolites	INORGANIC_zeolite	Silicalites, faujasites, etc
Zeolite Hill-Sauer	INORGANIC_zeolite_HS	silica, aluminasilicic acid, aluminosilicates
CHARMM19 - United atom model	CHARMM19	amino acids.
Gromos united atom G54A7	G54A7	Amino acids, lipids.
Non-specific, miscellaneous FF	MISC_FF	Anything: user define.
Multiple potential	multiple	Mixed components, bioinorganics.

Example below shows a top portion of an example control file, showing the CHARMM22 protein FF is used.

Control file title. For DL_FIELD 4.10.
1        * Construct DL_POLY output files
0        * Secodary output files (Gromacs, Chemshell or none).
charmm22_prot  * Type of force field require (see list below for choices).
kcal/mol  * Energy unit: kcal/mol, kJ/mol, eV, or K.
normal  * Conversion criteria (strict, normal, loose)
1        * Bond type (0=default, 1=harmonic , 2=Morse)
1        * Angle type (0=default, 1=harmonic, 2=harmonic cos)
...
...

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