Dear All,
I am trying to simulate a protein-peptide complex. the peptide is ~10
residues out of which 3 at one end are interacting with the protein. The
other end of the peptide is free to fluctuate. I ran a simulation of 10ns
and it was observed that the r.m.s.d of the coordinates generated during the
simulation becomes very high after ~2ns and progressively keeps rising after
that. This could indicate that something is not okay with the simulation.
Can you suggest what I can alter to stabilize the simulation?
Thanks,
Po
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Received on Thu Aug 04 2011 - 00:30:02 PDT
