[gmx-users] Regarding RMSD analysis result

[Felipe Pineda, PhD]

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?