pysimm.forcefield.gaff module

class pysimm.forcefield.gaff.Gaff(db_file=None)

Bases: pysimm.forcefield.forcefield.Forcefield

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

ff_name

gaff

pair_style

lj

ff_class

1

assign_atypes(s)

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

Parameters:s – System Returns:None

assign_btypes(s)

Gaff 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_charges(s, charges='gasteiger')

Charge assignment. Gasteiger is default for now.

Parameters:

• s – System
• charges – gasteiger

Returns:

None

assign_dtypes(s)

Gaff 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(s)

Gaff specific improper typing rules. There are none.

Parameters:s – System Returns:None

assign_ptypes(s)

Gaff 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