mstk.simsys.GromacsExporter

class mstk.simsys.GromacsExporter

GromacsExporter export a System to input files for Gromacs.

The following potential functions are currently supported:

Note that the Drude polarization in GROMACS have never been thoroughly tested. Use it with care.

In order to use GROMACS for trajectory analysis, the following potential functions can also be exported. But the exported files are only used to generate tpr file, which is required by most gmx analysis commands. Do NOT use the exported files for production simulations.

  • MieTerm will be exported in the LJ-12-6 form

  • MorseVdwTerm will be exported in the LJ-12-6 form

  • QuarticBondTerm will be exported in the harmonic form

  • QuarticAngleTerm will be exported in the harmonic form

  • SDKAngleTerm will be exported in the harmonic form

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) –