[gmx-users] About g_rms and the XPM file format

Víctor victor.gil.sepulveda at gmail.com
Mon Jan 23 14:56:19 CET 2012

Dear all,

I've been trying to do a rmsd matrix of  two different trajectories by
using g_rms (with -f traj1 and -f2 traj2). I'm wondering if the algorithm
g_rms uses does something like this:

for each frame f1 in traj1:
  for each frame f2 in traj2:
    superimpose f1 , f2
    calculateRMSD f1, f2

Or like this (as I've seen in some other rmsd matrix calculation scripts):

for each frame f in traj1:
  superimpose f with first frame

for each frame f1 in traj1:
  for each frame f2 in traj2:
    calculateRMSD f1, f2

I've also been trying to convert the resulting xpm file to a readable file
in order to process it using python. Is there any tool to do this kind of
conversion?(Btw I've been trying to find this kind of tool with not much
luck). There's enough info on the file to be able to parse it easily, but
using a 3rd party tested tool would be more convenient.



Víctor Gil Sepúlveda
E. Informatica - FIB - UPC
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