[gmx-users] Problem in RMSD plot

[Justin Lemkul]

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

-- 
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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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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