You don't tell us very much. For example which atoms are used in rmsd? It is
the part that you said is expected to fluctuate? Also, what did you do to
calculate rmsd? Did you use any sort of periodic imaging? Have you
visualized this trajectory to see what is happening? My rule is to always
look at your primary data (coordinates, through a viz program) and the do
numerical analysis to quantify what you see in the data. Never, ever skip
the step of actually looking at the molecule.
On Aug 4, 2011 3:00 AM, "Xiao Chen" <chen.xiao.po.gmail.com> wrote:
> 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 - 04:30:03 PDT
