Gromacs TOP file format

Classes

class gromacs.fileformats.top.TOP(fname)

Class to make a TOP object from a GROMACS processed.top file

The force-field and molecules data is exposed as python object.

Note

Only processed.top files generated by GROMACS ‘grompp -pp’ are supported - the usual topol.top files are not supported (yet!)

Initialize the TOP structure.

Arguments:

fname

name of the processed.top file

write(filename)

Write the TOP object to a file

class gromacs.fileformats.top.SystemToGroTop(system, outfile='output.top', multiple_output=False)

Converter class - represent TOP objects as GROMACS topology file.

Initialize GROMACS topology writer.

Arguments:

system

blocks.System object, containing the topology

outfile

name of the file to write to

multiple_output

if True, write moleculetypes to separate files, named mol_MOLNAME.itp (default: False)

assemble_topology()

Call the various member self._make_* functions to convert the topology object into a string

History

Sources adapted from code by Reza Salari https://github.com/resal81/PyTopol

Example: Read a processed.top file and scale charges

Run grompp -pp to produce a processed.top from conf.gro, grompp.mdp and topol.top files:

$ grompp -pp

This file now containts all the force-field information:

from gromacs.fileformats import TOP
top = TOP("processed.top")

Scale the LJ epsilon by an arbitrary number, here 0.9

scaling = 0.9
for at in top.atomtypes:
  at.gromacs['param']['lje'] *= scaling

Write out the scaled down topology:

top.write("output.top")

Note

You can use this to prepare a series of top files for Hamiltonian Replica Exchange (HREX) simulations. See scripts/gw-partial_tempering.py for an example.