[gmx-users] Problem in RMSD plot

Justin Lemkul jalemkul at vt.edu
Thu Jun 13 17:50:32 CEST 2013

On 6/13/13 10:47 AM, Sainitin Donakonda wrote:
> Hi,
> Recently i ran 20ns protein ligand simulation ..in cluster ..I ran it in 2
> parts first i ran 10ns and extended to another 10ns..
> Then I got 2 .xtc files...i combined both these trajectories using
> following command
> trjcat -f 1.xtc 2.xtc -o combine.xtc -cat
> Then using combine.xtc i plotted RMSD plot for protein back bone i got the
> plot but it is strange there is a line from 0 ns passing as daignol
> Here i attach that plot..
> Can any body suggest how to solve this issue..

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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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