scripts for analyzing molecular dynamics trajectories using VMD

Scripts will run the analysis given a .gro and .xtc/.trr file. (It's expecting GROMACS output, but could be easily tweaked for other sorts of MD package otuput).

Most analysis directories (say local-rmsd) have an associated tcl file (say local-rmsd.tcl)= that is actually passed through vmd, which will spew out a vast quantity of incomprehensible input. local-rmsd.py then processes this input and spits it out in a human (and "R") readable format. The analysis can be run on multiple files using the run-me.sh script that is in each directory. Analysis directories sometimes have an associated .R file for plotting and/or doing further analysis.