[gmx-users] problem about rmsd

Justin A. Lemkul jalemkul at vt.edu
Fri Mar 21 17:43:54 CET 2008

Quoting sudheer babu <sudheer.pbm07 at gmail.com>:

> Hi all,
> I gave 1ns run production step without velocities in md.mdp file, in between
> my simulation crashed, so I used *tpbconv for continue that crashed run ,
> After finishing that I used *trjcat for catenation of my 2 simulation
> trajectory files, its shown only 900ps trajectory files into trjout.xtc not
> 1000ps without error.  By using this I plotted rmsd its shown that only
> 900ps values graph.
> what could be the reason for not getting 1000ps trajectory values, pls give
> me suggestion,
> Thanks in advance.

In the absence of your exact command lines, we can only assume that you have
used the tools incorrectly.  Provide the commands you issued and we might be
able to help.



Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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