[gmx-users] MSD and merging trajectory files

Lars Poulsen lpoulsen at chem.au.dk
Wed Jan 16 17:01:28 CET 2002

Since I'm not an expert at C code I was wondering, if anyone on the list could enlighten me about the MSD routine in GROMACS: g_msd.
I looks to me like g_msd is calculating <|r(t)-r(0)|>^2 averaged over the molecules/atoms in the given group - which is all fine. However, it seems to operate with only one time origin (t=0), which is not so fine when you want to improve statistics. (from the output: the 'noise level' is constant over time and it has sharp jumps)  Is this observation correct?
Is there a flag for g_msd I have overlooked? Or should I use g_analyse instead? Or somethingelse?

Because of some instabilities in my linux system, I had to restart my md-simulation several times using tpbconv. Initially, I thought mdrun would then continue writing in the same trajectory files as before, but this appears not to be the case. So now I have several traj. files, that I would like to merge into one. Is there an utility for that in GROMACS?

mvh Lars
Lars Poulsen
Dept. of Chemistry, University of Aarhus
Langelandsgade 140, DK-8000 Aarhus C
Phone: +45 8942 3871
Fax: +45 8619 6199
email: lpoulsen at chem.au.dk

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