[gmx-users] g_msd Time Unit

[Fotis Baltoumas]

Hello Tim,

In GROMACS trajectories, the simulation time is normally saved alongside 
the coordinates in the trr and xtc files as produced by GROMACS itself. 
That's how the various analysis tools can understand time when it is 
required.

However, NAMD does not save the simulation file in the DCD format; that 
information is contained exclusively in the logs. Therefore, when you 
converted your trajectory to the trr format (I assume you used catdcd), 
you just saved coordinates, not timesteps.

To add timestep information in your trajectory you should, prior to 
analysis, perform another manipulation with trjconv, using the "-t0" and 
"-timestep" options properly.


For example, if you have a file called "traj.trr" that has 5000 frames, 
starting at 0 ps with each frame recorded every 10 ps, you should do 
something like the following :

trjconv -f traj.trr -s structure.pdb -o traj_time.xtc -t0 0 -timestep 10

(I assume you use Gromacs 4.x or earlier, since you reference "g_msd" 
instead of "gmx msd", otherwise, use "gmx trjconv").

Then use the result, traj_time.xtc as input for g_msd.

Hope this helps,

Fotis Baltoumas


-- 
Fotis A. Baltoumas, Bsc, Msc
Phd Candidate, Bioinformatics Postgraduate Programme
Section of Cell Biology and Biophysics
Department of Biology
National & Kapodistrian University of Athens
Panepistimiopolis, Athens 157 01, GREECE
    --------------------------------------

email : fbaltoumas at biol.uoa.gr
http://biophysics.biol.uoa.gr
http://bioinformatics.biol.uoa.gr
Tel.: +30 2107274876
Mob.: +30 6979258570



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