[gmx-users] g_msd : input files question

[Nuno Ricardo Loureiro Ferreira]

Hello all

First time, in this list.
I'm a namd user. Searching the net for scripts to analyze the MD
trajectories, and to calculate the mean squared displacement (MSD) of my
system, I've encontered some good scripts in the gromacs software pack,
namely g_msd .
Since I have .dcd (binary trajectories) and .psf (structure file in X-PLOR
format) files, I would like to know if its possible to analyze my MD run's
within GROMACS.
To run the g_msd, I need a trajectory file (which I already have, dcd -->
ttr), and a "Structure + mass (db) : tpr tpb tpa gro g96 pdb" like file.
I converted the .dcd to .ttr (using the trio program, from namd webpage). Is
it possible to obtain the second file from my .psf file?
Any help with this, will be greatly appreciated.
Best regards,
Nuno


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Nuno Ricardo Santos Loureiro da Silva Ferreira
Grupo de Química Biológica
Departamento de Química
Faculdade de Ciências e Tecnologia
Universidade de Coimbra
3004-535 Coimbra
Portugal

Phone: +351 239 852080
Fax: +351 239 827703
www.biolchem.qui.uc.pt
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