mstk.simsys.GromacsExporter

class mstk.simsys.GromacsExporter

GromacsExporter export a System to input files for Gromacs.

The following potential functions are currently supported:

• LJ126Term

• HarmonicBondTerm

• HarmonicAngleTerm

• LinearAngleTerm

• OplsDihedralTerm

• PeriodicDihedralTerm

• OplsImproperTerm

• HarmonicImproperTerm

• DrudeTerm

The MieTerm can be exported, but it will be in the LJ-12-6 form. If the dispersion of MieTerm is in 6-th power, then MieTerm can be correctly handled by small modifications to topol and mdp files after exported. Refer to the GROMACS documentation for details.

The SDKAngleTerm can be exported, but it will be in the harmonic form. Usually it is acceptable if the molecule is not going to form a coil structure. Refer to the original SDK paper for details.

Methods

__init__()
export(system, gro_out, top_out, mdp_out, ...)	Generate input files for Gromacs from a system

static export(system, gro_out, top_out, mdp_out, **kwargs)

Generate input files for Gromacs from a system

# TODO Export virtual sites other than TIP4P

Parameters:

• system (System) –

• gro_out (str or None) –

• top_out (str or None) –

• mdp_out (str or None) –