[gmx-users] disparity in RMSD calculation

Yongchul Chung yxc169 at case.edu
Sat Nov 20 07:13:51 CET 2010

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
> 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.


> Thanks for any suggestion.
> Sunita
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