Some scripts I’ve written for my research might be useful for someone else, so I store them in my github repository. On this page I introduce some of them. Feel free to use and modify.

Xvg scripts

Simple scripts for modifying xvg-files (multi-column data file format used in Gromacs). My plan is to merge these scripts into one “swiss army knife of xvg-tools” at some point…
Simple read/write module to import xvg-file as NumPy array
Merge order parameter graphs for saturated and unsaturated atoms produced by g_order (a Gromacs tool).
Find the intersection point of two graphs.
Join two xvg-files.
Cumulative sum of columns.
Mirror graph.
Moving average of graphs.
Scale x- or y-axis.

Fine grain

Map files for fine graining coarse grained Martini lipids to OPLS using backward-script:

Automatically initialize umbrella sampling simulations.
Split GROMACS index.ndx file in half based on molecule coordinates.
Checks the R/S-handedness of molecules stereocenters based on the coordinates of the chiral center and four atoms bound to it.
Use FFMPEG to create high quality video from ppm-images produced by VMD