Scripts

pmx provides a few command line scripts that can be used to setup and analyse free energy calculations. After installing the library, pmx should be in your $PATH. You can check this with the following command.

$ which pmx

The pmx help will show the scripts available.

$ pmx -h
usage: pmx [-h]

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 pmx command line scripts
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 Available commands are:
     mutate       Mutate protein or DNA/RNA
     gentop       Fill hybrid topology with B states
     analyse      Estimate free energy from Gromacs xvg files

     doublebox    Place two input structures into a single box
     abfe         Setup files for an ABFE calculation

     genlib       Generate pmx ff library
     gmxlib       Show/set GMXLIB path

 optional arguments:
     -h, --help  show this help message and exit

A description of these scripts can be found here:

• Mutate
• Gentop
• Analyse
• Genlib

In the Examples you can find instead how the same tasks can be carried out using the API.