DL_FIELD
DL_FIELD is an external tool that can generate classical forcefields. When integrated with ChemShell, it can be used to generate the forcefields needed for QM/MM models directly. DL_FIELD is free for academic users and the registration form is available here https://www.ccp5.ac.uk/dl_field-registration/. Presently, the use of DL_FIELD is only supported in combination with DL_POLY as the MM theory.
DL_FIELD makes a distinction between organic and inorganic forcefields.
- class DL_FIELD
General options
- dl_poly
(default:
True) Generate output forcefields in DL_POLY FIELD format
- ff
Forcefield (ff) scheme. The options available will depend on the version of DL_FIELD.
Allowed values:
'CHARMM': (default) All-atom CHARMM'CHARMM22_prot': CHRMM22 for proteins'CHARMM36_prot': CHARMM36 for amino acids, proteins'CHARMM36_nucl': CHARMM36 for nuclei acids'CHARMM36_lipid': CHARMM36 for lipids'CHARMM36_carb': CHARMM36 for carbohydrates'CHARMM36_cgenff': CHARMM general force field'CHARMM19': United-atom for CHARMM'AMBER': All-atom Amber'AMBER16_gaff': AMBER general force field'OPLSAA': OPLS-AA'OPLS2005': OPLS_2005'OPLS_AAM': OPLS AA/M for proteins'OPLS_CL_P': CL&P for ionic liquids'OPLS_DES': OPLS for deep eutectic solvent'DREIDING': DREIDING'PCFF': Polymer consistent force field'CVFF': Consistent Valence Force Field'COMPASS': COMPASS force field'TRAPPE_EH': Transferable potentials (explicit hydrogen) for phase equilibria'TRAPPE_UA': Transferable potentials (united atom) for phase equilibria'G54A7': Gromos united atom G54A7'INORGANIC_binary_oxide': Inorganic FF for binary oxides'INORGANIC_ternary_oxide': Inorganic FF for ternary oxides'INORGANIC_binary_halide': Inorganic FF for binary halides'IORGANIC_glass': Inorganic FF for glass'INORGANIC_clay': Inorganic FF for clay'INORGANIC_zeolite': Inorganic FF for zeolite'INORGANIC_zeolite_HS': Zeolite Hill-Sauer'MISC_FF': Non-specific, miscellaneous FF'multiple': Multiple potential
Note
This list is for version 4.12 of DL_FIELD
- unit
Energy unit for the output forcefield file
Allowed values:
'kcal/mol': (default) Kilocalorie per mole'eV': Electron volts'kJ/mol': Kilojoule per mol'K': Kelvin
- conversion
DL_FIELD determines the bond connections of a molecule based on atomic distance criteria, where a bond is identified if two atoms are within a certain minimum distance.
Allowed values:
'normal': (default) Default distance criteria used to identify bonds.'strict': Distance for bond indentification is reduced by 0.01 Å.'loose': Distance for bond indentification is increased by 0.01 Å.
- udff
(default:
None) Name of User-defined Force Field (udff) file, as described in the DL_FIELD manual. DL_FIELD udff files are used to add new paramaters and molecular templates to DL_FIELD, and will overwrite information in DL_FIELD’s internal library files.
- verbosity
(default:
True) Verbosity mode. When this is switched on, DL_FIELD will display detailed conversion process information, including the converted atom types.
- input
- output
- optimise
(default:
True) If the output forcefield file should be optimised by DL_FIELD.
- override_builtin
(default:
False) Specifies whether user-defined parameters should override those of the standard forcefield.
- atom_display
ATOM_KEY display format. This setting allows user to select the display format for the ATOM_KEYs in FF files generated by DL_FIELD.
Allowed values:
'standard': (default) standard format according to the type of potential scheme selected'dl_field': dl_f_notation atom notation
- vdw_format
(default
'12-6')
- eps_org
(default
'arithmatic')
- sig_org
(default
'arithmatic')
- eps_diff
(default
''arithmatic')
- sig_diff
(default
''arithmatic')
- extra_info
(default
False) Display additional information (for DL_POLY FF files only). This setting allows the option to display additional information in a PDB file in dl_poly.CONFIG and dl_poly.FIELD files, such as the amino acid residue sequence obtained from the user’s protein PDB file.
- freeze
- tether
- constrain
- rigid_body
- pbc
(default: 0) Periodic boundary conditions.
- scale_coul
(default:
'default') 1-4 scaling for coulombic interaction
- scale_vdw
- recentre
- distance
- min_distance
- mm_energy
- cutoff_coulomb
- cutoff_vdw
- filename
(default:
'_dl_field.pdb')
- exclude
(default:
[])
- qmatoms
(default:
[])
- solvents
(default:
[])
- remove_unused_definitions
(default:
True) Remove unused residue entries.
- original_tip3p
(default:
False) Use the original TIP3P water model (rather than the default, TIP3P modified for CHARMM)
- directory
(default:
'_dl_field') Archive directory name for DL_FIELD inputs and outputs.
- field_by_chemsh
(default:
True) We deal with the QM/MM special treatments with ChemShell instead of DL_FIELD
- run_only_once
(default:
True) Run DL_FIELD only for the first step of an optimisation (otherwise DL_FIELD will be run every step). This option should be used when the forcefield is not expected to be updated as atoms move in the simulation.
- patch_target
(default:
{}) Dictionary containing targets for patching fragments.
Organic ff options
- sig_org
Specify mixing rule for the parameter sigma (steric parameter) for LJ12-6 between two atoms.
Allowed values:
'arithmatic': (default)'geometric':'default':
Inorganic ff options
The following options only apply to DL_FIELD’s inorganic forcefields
- eps_inorg
Specify mixing rule for the parameter epsilon (potential well-depth) for LJ12-6 between two atoms.
Allowed values:
'geometric': (default)'arithmatic':
- sig_inorg
Specify mixing rule for the parameter sigma (steric parameter) for LJ12-6 between two atoms.
'geometric': (default)'arithmatic':
Dreiding ff options
The following options are specific to the Dreiding forcefield.
- bond
Dreiding bond type.
Allowed values:
'harmonic': (default) Harmonic bond'morse': Morse bond
- angle
Dreiding angle type.
Allowed values:
'harmonic': (default) Harmonic angle'cos': Harmonic cos angle
Initial velocities options
- velocity
(default:
False) Assign initial Gaussian random velocities, scaled to a temperature, to every atom in the output dl_poly.CONFIG file.
- temperature
(default:
300.0) Temperature for initial velocities.
Solvation options
The following options only apply to DL_FIELD’s solvation functionality
Warning
The solvation features of DL_FIELD are not supported by ChemShell
- solvent
- solution
Solution Maker on/off
- solution_den
Solution Maker density
- solution_unit
Solution Maker unit
- solution_cutoff
Solution Maker cutoff
- counterions
Add counter ions