[gmx-users] disparity in RMSD calculation

[Sunita Patel]

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
> -- 
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Dr. Sunita Patel
---------------------------------------------
Visiting Fellow
Department of Chemical Sciences
T.I.F.R., Homi Bhabha Road, Colaba
Mumbai - 400005
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