Gromacs parameter MDP file format

The .mdp file contains a list of keywords that are used to set up a simulation with Grompp. The class MDP parses this file and provides access to the keys and values as ordered dictionary.

class gromacs.fileformats.mdp.MDP(filename=None, autoconvert=True, **kwargs)

Class that represents a Gromacs mdp run input file.

The MDP instance is an ordered dictionary.

• Parameter names are keys in the dictionary.
• Comments are sequentially numbered with keys Comment0001, Comment0002, ...
• Empty lines are similarly preserved as Blank0001, ....

When writing, the dictionary is dumped in the recorded order to a file. Inserting keys at a specific position is not possible.

Currently, comments after a parameter on the same line are discarded. Leading and trailing spaces are always stripped.

See also

For editing a mdp file one can also use gromacs.cbook.edit_mdp() (which works like a poor replacement for sed).

Initialize mdp structure.

Arguments:

filename

read from mdp file

autoconvert : boolean

True converts numerical values to python numerical types; False keeps everything as strings [True]

kwargs

Populate the MDP with key=value pairs. (NO SANITY CHECKS; and also does not work for keys that are not legal python variable names such as anything that includes a minus ‘-‘ sign or starts with a number).

read(filename=None)

Read and parse mdp file filename.

write(filename=None, skipempty=False)

Write mdp file to filename.

Keywords:

filename

output mdp file; default is the filename the mdp was read from

skipempty : boolean

True removes any parameter lines from output that contain empty values [False]

Note

Overwrites the file that the mdp was read from if no filename supplied.