On 01/24/11, Archana Sonawani <[email protected]> wrote: > Hello, > > > > 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. > > > > These are almost certainly periodicity artefacts. Look at your trajectory in a suitable visualization algorithm, and you will see (parts of) the complex cross boundaries at those points. See http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions for discussion and solution approaches.
Mark > > >
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