Re: diffusion / fex peptide problem

From: Roman Petrenko (
Date: Wed May 06 2009 - 12:33:49 CDT

Dear Ben,
what else did you expect? water expels hydrophobic parts of your
peptide to the vacuum.
use periodic boundary conditions, so that there is no vacuum in the system.

On Wed, May 6, 2009 at 11:24 AM, Benjamin Stauch <> wrote:
> Dear community,
> I plan to run quite long (hundreds of nanoseconds) simulations of a small
> peptide. In the first attempts, the peptide quickly leaves the center of the
> solvent sphere (I use spherical boundary conditions) and diffuses to the
> surface, resulting in partial "vacuum" contact of the peptide.
> As I don't want this to happen, and the sphere already has plenty of
> cushion, and I expect molecules of that size to diffuse quickly, I would
> like to ask if there might be a simple workaround to that problem. Funny
> enough, I was not really able to find something useful in documentation and
> mailing list archive (either it's too obvious or does not happen to proteins
> that easily).
> I know that removing the velocity of the center of mass of the sphere only
> works on its initial velocity and thus will not help. Is it worth trying to
> fix a single atom in the peptide (still calculating forces on it), as the
> sphere center itself is defined and should not move? Or would applying
> periodic boundary conditions circumvent the problem? I'm a bit hesitant to
> do that as I'm not sure about the wrapping of the individual atoms; I need
> to work on the molecule's cartesian coordinates, so in case of periodic
> boundary conditions I would better not wrap them in order to not disrupt the
> molecule?
> Thanks and all the best,
> Ben

Roman Petrenko
Physics Department
University of Cincinnati

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