Hi,
> I am trying to simulate a protein-peptide complex. the peptide is ~10
...
> that. This could indicate that something is not okay with the simulation.
This is a good point at which to check out if something actually is wrong
with your simulation. Plot not only rmsd but also rmsf to see if
fluctuations are happening in only some parts of the system. Is the
peptide-protein interaction, e.g. H-bonds etc, maintained? How stable do
you think the system should be?
What you could see is a bad initial model that merely would take very long
to equilibrate. Where do your starting coordinates come from and how
reliable are they?
> Can you suggest what I can alter to stabilize the simulation?
You could add restraints to part of your system, making them more stable,
but then you are biasing your simulation, maybe so much that you cant
learn anything from it anymore...
Kind Regards,
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Thu Aug 04 2011 - 01:00:03 PDT
