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

[lina]

On Mon, Jan 23, 2012 at 9:56 PM, Víctor <victor.gil.sepulveda at gmail.com> wrote:
> 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

BTW, xpm file is readable.
try:
more xpm or other tools your preferred to read.


> 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.
>
> Thanks!
>
> --
>
> Víctor Gil Sepúlveda
> E. Informatica - FIB - UPC
>
> --
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