[gmx-users] disparity in RMSD calculation

Sunita Patel sunita at mailhost.tifr.res.in
Sat Nov 20 07:51:04 CET 2010

On Sat, 20 Nov 2010 01:13:51 -0500, Yongchul Chung wrote
> On Sat, Nov 20, 2010 at 12:54 AM, Sunita Patel <sunita at 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.
> Greg
> Thanks for any suggestion.
> Sunita
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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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