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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