[gmx-users] Problem in RMSD plot

Sainitin Donakonda saigro16 at gmail.com
Thu Jun 13 16:47:37 CEST 2013


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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