[gmx-users] Regarding RMSD analysis result
Felipe Pineda, PhD
luis.pinedadecastro at lnu.se
Tue Sep 25 10:45:52 CEST 2012
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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