[gmx-users] problem about rmsd

[Justin A. Lemkul]

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



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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

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