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

[Víctor]

I've having some problems with use of the option '-fitall'.

The command I'm using is:
g_rms -hidden -fitall -s ../topol_amber.tpr -f ../amber99sb_skip10.xtc -f2
../amber99sb_skip10.xtc -m rmsd.xpm

But a diff with the rmsd.xpm file I got without using '-fitall' reveals
that the files are identical.

Furthermore, the rmsd.xpm file represents a non-symetric matrix, which is
not what I expected... Anyone has a clue of what's happening?

Thanks in advance,
Víctor

On Mon, Jan 23, 2012 at 5:12 PM, Víctor <victor.gil.sepulveda at gmail.com>wrote:

> Yes, thanks. My first impulse was to do a python script to do the
> conversion, but Tsjerk Wassenaar's script works neat :)
>
> On Mon, Jan 23, 2012 at 5:10 PM, lina <lina.lastname at gmail.com> wrote:
>
>> 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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>
>
>
> --
>
> Víctor Gil Sepúlveda
> E. Informatica - FIB - UPC
>



-- 

Víctor Gil Sepúlveda
E. Informatica - FIB - UPC
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