On Sat, 20 Nov 2010 01:13:51 -0500, Yongchul Chung wrote > On Sat, Nov 20, 2010 at 12:54 AM, Sunita Patel <sun...@mailhost.tifr.res.in> > 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.
Still, am getting the same plot in gmx even after removal of periodic boundary conditions. Visual observation of trajectory on VMD is more similar to the RMSD am getting from VMD. My worry is that why gmx is not giving the similar result. Thanks Greg. Any suggestion will be appreciated. Sunita > > Greg > > Thanks for any suggestion. > Sunita > > > -- > gmx-users mailing list gmx-us...@gromacs.org > 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 gmx-users-requ...@gromacs.org. > 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 ---------------------------------------------
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