Re: writing back coordinates of waters that cross the unit cell

From: Axel Kohlmeyer (
Date: Thu Nov 25 2010 - 09:07:55 CST

On Thu, Nov 25, 2010 at 9:29 AM, kakali sen <> wrote:
> Dear All,
> I am running a NPT simulation, now as the simulation proceeds, the protein
> is translated towards y-direction. I had tcl forces on for initial 30 ns and
> and later removed it. I am using wrapall and wrapwater in my simulation so
> the protein and water is wrapped back to the unit cell however the protein
> is floating. I have COMmotion is set to zero. I suppose the fluctuations are
> arising from the use of harmonic forces via TCL force.
> For further work I wold like to cut out different water spheres around the
> protein from a snapshot, So I would need a buffer of water around the
> protein.
> Is there any way by which the center of mass motion can be updated more
> frequently so that this translational motion can be avoided. Or is any way

you can do this after the fact using the pbctools plugin in VMD.
just select your protein as reference for the center and the waters
are going to be wrapped around it in the optimal way.


> to get rid of this extra translational motions. If not, then is there a
> possibility to translate the whole system (without disturbing the internal
> hydration pattern of the protein) to the original center of mass so that I
> have more or less equivalent buffer around the protein to cut out external
> shells of water.
> Any suggestions will be highly appreciated?
> thanks in advance.
> kakali

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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