[gmx-users] disparity in RMSD calculation

[Mark Abraham]

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