[gmx-users] Query for RMSD

Archana Sonawani ask.archana at gmail.com
Mon Jan 24 06:46:52 CET 2011


I have run 10 ns simulation for ligand-receptor complex. For analysis, I
checked RMSD, Radius of gyration, Hydrogen bonds and distance using g_dist.

In the RMSD plot, the whole simulation shows RMSD between 0 - 0.5nm , but
after 5ns I get long vertical lines upto 2.5 nm. I dont know whats the
reason for that. I am sending the RMSD plot as attachment.
These lines are not seen in case of hydrogen bond plot and distance plot.
Please help me out.



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