[gmx-users] g_msd : input files question

[David]

On Mon, 2003-04-28 at 22:17, Nuno Ricardo Loureiro Ferreira wrote:
> 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.

I think a pdb file will do, you can probably generate that someway or
antoher. If you have that you can use to select subsets of your system
(e.g. oxygen in water) using the make_ndx program. This will generate a
.ndx file that you feed to g_msd again.



> Best regards,
> Nuno
> 
> 
> #######
> 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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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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