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Miscelaneous scripts This repository is meant to contain (hopefully) helpful script for assorted work.

Contents

Scripts

gmx_log_processor.py

Takes a .log file from a GROMACS mdrun simulation and makes a comma-separated-values (.csv) file of energy values that can be used for plotting in Microsoft Excel,R, MatPlotLib and the like.

Example run

python3 gmx_log_processor.py -i my_md.log -o my_md.csv ... where -i is for input and -o for output

A simpler (and likely better) alternative to this script

Justin A. Lemkul at VirginiaTech suggests that providing the -xvg none flag to gmx energy is a much easier way of getting this information: gmx energy -f my_em.edr -o potential.xvg -xvg none

History

This script was developed in August 2020 when the [https://plasma-gate.weizmann.ac.il/Grace/](Xmgrace website) failed for some unknown reason. I developed this script as a replacement, for my own use, to parse the mdrun output from GROMACS and give out tables of energy values that can be easily plotted in e.g. Excel. Again: the Grace website was broken, I needed to analyse mdrun output, so I wrote this script. Feel free to use it, but please note the warnings at the end!

Installing for long-term usage

You can remove the 'python3' and turn this script into recognisable software that you can run from anywhere in your system by doing the following:

  1. Make the script executable by executing the following in the shell: chmod 755 gmx_log_processor.py

  2. Put it in a place where your shell can find it, e.g. you could make a directory called bin and put your executable scripts there, then add that directory to your $PATH variable. So, at your own risk and discretion, you could add this line to your .bash_profile, .bashrc, .zshrc, or whichever approriate file controls your shell sessions: PATH=$PATH:/Users/MyUserName/MySoftware/bin Where that directory is whichever directory you want to put this script in.

  3. Edit the first line of this script to make sure it points to wherever your python3 is. You can normally find out by running: which python3 If your system can't find python3, you probably don't have it installed, but hopefully you'll see something like: /Users/MyUserName/opt/anaconda3/bin/python3 OK, now the script should be findable and executable.

  4. Optional: you could remove the .py from the name, so that it looks more like a command. Go to wherever you put the script and change its name: mv gmx_log_processor.py gmx_log_processor ... and now you should be able to run it from anywhere like this: gmx_log_processor -f my_md.log -o my_md.csv

⚠️ Warnings ⚠️

🚧 Please consider this script a under construction 🚧

The script is provided "as is" and I take absolutely no responsibility for anything that goes wrong, e.g. if it gives you incorrect results, deletes your data, or whatever.

It hopefully shouldn't do any of those things, though! And on that note, if you do find a bug, I would be very grateful if you could please point me to it so that I can fix it as soon as possible. Same if you find a way to improve it and want to collaborate.

In any case:

🚨 I STRONGLY recommend that you check at least a few values in your input .log file to make sure they match those in the output of the .csv file that the script produces. 🚨