On Sat, 20 Nov 2010 19:05:35 +1100, Mark Abraham wrote > On 20/11/2010 4:54 PM, Sunita Patel 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? > > > > We can't be definitive without more detail of your two methods. The > jumps look like differing PBC treatments. See trjconv -h for ways to > choose how they are treated. Note that the "non-jumped" parts of the > GROMACS curve agree with the VMD one.
Thanks Mark. With non-jumped trajectory also am getting same RMSD plot. Sunita > > Mark > -- > 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 Dr. Sunita Patel --------------------------------------------- Visiting Fellow Department of Chemical Sciences T.I.F.R., Homi Bhabha Road, Colaba Mumbai - 400005 --------------------------------------------- -- 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
