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: [email protected] > To: [email protected] > 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 [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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