With topol.tpr file, am getting identical plot as that of VMD. Thanks, Sunita
On Sat, 20 Nov 2010 08:39:17 +0000, X Rules wrote > I have had a similar experience, I have not investigated it thoroughly at the > moment, but I get different (identical with specific jumps possibly due to > pbc) plots if I take starting structure as my input pdb file or if my > starting structure is first structure of trajectory. > > I think the plots would be fine if you just use g_rms -s topol.tpr -f > traj.xtc > > > Date: Sat, 20 Nov 2010 19:05:35 +1100 > > From: mark.abra...@anu.edu.au > > To: gmx-users@gromacs.org > > Subject: Re: [gmx-users] disparity in RMSD calculation > > > > 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. > > > > Mark > > -- > > gmx-users mailing list gmx-users@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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