On Sat, Nov 20, 2010 at 12:54 AM, Sunita Patel <[email protected]>wrote:
> Dear Users, > > I calculated RMSD for a trajectory with same reference structure using > GROMACS > and VMD. I observed completely difference plots for the same data. Please > see > the attached file. > > What could be the cause for this disparity? > it is hard to predict what is causing the disparity without what you typed in the terminal, and your system. Perhaps check if you've removed the periodic boundary conditions when calculating the rmsd in gmx by invoking -nopbc option. Greg > > Thanks for any suggestion. > Sunita > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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