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
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