Re: Only part of the protein is moving in MD simulation

From: Leandro Martínez (
Date: Wed Oct 26 2005 - 10:58:19 CDT

If you are using harmonic constraints on the protein atoms why do you expect
them to move? It is not clear from your mail. Anyway, I'm running 10 ns
dynamics at high temperature and even then the protein does not move too
much. Proteins are quite rigid at these time-scales.

On 10/26/05, Uma Mahankali <> wrote:
> Hello,
> I am running a simulation of a membrane protein in water box with PBC and
> I imposed a harmonic constraint of 0.5 kcal/mol on the protein atoms. Even
> after 1 ns of equilibration, only the bottom part of the protein has moved a
> bit and the top part has not moved at all. I am suspecting that it could be
> because of high pressure (I am running an NVT simulation).
> Has anyone observed such a trend before?
> Thanks,
> Uma
> --
> Uma Mahankali,
> Graduate Student,
> Department of Chemistry,
> University of Cincinnati,
> Ohio-45219

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