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<font size="2">With topol.tpr file, am getting identical plot as that of VMD.
<br />Thanks,
<br />Sunita
<br />
<br />
<br />On Sat, 20 Nov 2010 08:39:17 +0000, X Rules wrote
<br />>
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.
<br />>
<br />> I think the plots
would be fine if you just use g_rms -s topol.tpr -f traj.xtc
<br />>
<br />>
> Date: Sat, 20 Nov 2010 19:05:35 +1100
<br />> > From:
Mark.Abraham@anu.edu.au
<br />> > To: gmx-users@gromacs.org
<br />> >
Subject: Re: [gmx-users] disparity in RMSD calculation
<br />> >
<br />>
> On 20/11/2010 4:54 PM, Sunita Patel wrote:
<br />> > > Dear
Users,
<br />> > >
<br />> > > I calculated RMSD for a trajectory
with same reference structure using GROMACS
<br />> > > and VMD. I
observed completely difference plots for the same data. Please see
<br />> >
> the attached file.
<br />> > >
<br />> > > What could be the
cause for this disparity?
<br />> > >
<br />> >
<br />> > We can't
be definitive without more detail of your two methods. The
<br />> > jumps
look like differing PBC treatments. See trjconv -h for ways to
<br />> >
choose how they are treated. Note that the "non-jumped" parts of the
<br />>
> GROMACS curve agree with the VMD one.
<br />> >
<br />> >
Mark
<br />> > --
<br />> > gmx-users mailing list
gmx-users@gromacs.org
<br />> >
http://lists.gromacs.org/mailman/listinfo/gmx-users
<br />> > Please search
the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before
posting!
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<br />
<br />
<br />Dr. Sunita Patel
<br />
---------------------------------------------
<br />
Visiting Fellow
<br />
Department of Chemical Sciences
<br />
T.I.F.R., Homi Bhabha Road, Colaba
<br />
Mumbai - 400005
<br />
---------------------------------------------
<br />
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