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

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Jan 23 15:39:27 CET 2012

Hi Victor,

By default it does this:

> 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

But there's a hidden option -fitall that gives you the other. Check

g_rms -h -hidden

> 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.

I posted a python script some while ago to do:


Hope it helps,


Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

More information about the gromacs.org_gmx-users mailing list