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
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