Installation¶

Clone the source code from GitHub with:

$ git clone https://github.com/deGrootLab/pmx.git

Then:

$ cd pmx
$ pip install .

Software requirements:

python >= 3.6
numpy
scipy
matplotlib

GMXLIB¶

In order to be able to use the hybrid/alchemical force fields available in pmx, the environment variable $GMXLIB needs to be set. You can either set $GMXLIB in each of you shell sessions when you want to use pmx, or you can set the variable directly in your ~/.bashrc file.

The pmx gmxlib command will tell you where the force field libraries were installed, and optionally allow you to automatically add $GMXLIB to your bashrc file.

$ pmx gmxlib

In order to be able to use the hybrid/alchamical force fields
available in pmx, the environment variable GMXLIB needs to be set.

The path to your pmx force field library is the following:
/path/to/your/pmx/data/mutff

You can either set GMXLIB in your shell session as follows:
$ export GMXLIB=/path/to/your/pmx/data/mutff

Or you can add this directly in your bashrc file.

Do you wish pmx to set the GMXLIB variable in your ~/.bashrc? [yes|no]
>>>

Alternatively, you can set the variable only for a certain python process using the set_gmxlib() function:

>>> from pmx.gmx import set_gmxlib
>>> set_gmxlib()