pysimm.forcefield.gaff2

Module Contents

class pysimm.forcefield.gaff2.Gaff2(db_file=None)

Bases: pysimm.forcefield.forcefield.Forcefield

pysimm.forcefield.Gaff2

Forcefield object with typing rules for Gaff2 model. By default reads data file in forcefields subdirectory.

ff_name

gaff2

pair_style

lj

bond_style

harmonic

angle_style

harmonic

dihedral_style

fourier

improper_style

cvff

ff_class

1

assign_ptypes(self, s)

pysimm.forcefield.Gaff2.assign_ptypes

Gaff2 specific particle typing rules. Requires System object Particle objects have bonds defined. * use System.add_particle_bonding() to ensure this *

* Not entirely inclusive - some atom types not used *

Parameters:s – System Returns:None

assign_btypes(self, s)

pysimm.forcefield.Gaff2.assign_btypes

Gaff2 specific bond typing rules. Requires System object Particle objects have bonds, type and type.name defined. * use after assign_ptypes *

Parameters:s – System Returns:None

assign_atypes(self, s)

pysimm.forcefield.Gaff2.assign_atypes

Gaff2 specific angle typing rules. Requires System object Particle objects have bonds, type and type.name defined. * use after assign_ptypes *

Parameters:s – System Returns:None

assign_dtypes(self, s)

pysimm.forcefield.Gaff2.assign_dtypes

Gaff2 specific dihedral typing rules. Requires System object Particle objects have bonds, type and type.name defined. * use after assign_ptypes *

Parameters:s – System Returns:None

assign_itypes(self, s)

pysimm.forcefield.Gaff2.assign_itypes

Gaff2 specific improper typing rules.

Parameters:s – System Returns:None

assign_charges(self, s, charges='gasteiger')

pysimm.forcefield.Gaff.assign_charges

Charge assignment. Gasteiger is default for now.

Parameters:

• s – System
• charges – gasteiger

Returns:

None