[gmx-users] Problem in RMSD plot

[Sainitin Donakonda]

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..

Thanks,
Nitin