[gmx-users] g_msd Time Unit

[Timothy Cholko]

Extremely helpful! Thanks

On Wed, Feb 6, 2019 at 3:29 AM Fotis Baltoumas <fbaltoumas at biol.uoa.gr>
wrote:

> 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
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>
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