[gmx-users] Regarding RMSD analysis result

Archana Sonawani ask.archana at gmail.com
Tue Sep 25 11:46:49 CEST 2012


Your RMSD graph is ok but is represented wrong due to pbc problem. Use
whole and nojump options of trjconv.

On Tue, Sep 25, 2012 at 2:15 PM, Felipe Pineda, PhD <
luis.pinedadecastro at lnu.se> wrote:

> On 09/25/2012 10:08 AM, naga sundar wrote:
>> Dear Felipe
>>                  Thanks for ur reply.
>>           The system is a protein-protein complex. Like u r saying its due
>> to pbc problem then why any abnormality  doesn't happened to the native
>> complex (Black line)?.
> Maybe because MD is stochastic ...
>    As already suggest by justin i checked  the pbc
>> conditions upto my knowledge everything is fine.
> As Justin said, it's not about the pbc conditions as they appear in the
> mdp file, but about pbc effects due to a chain, probably the ligand,
> leaving the box and being reflected to the opposite side. Have you checked
> out visually how the weird frames look like?
> --
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