writing back coordinates of waters that cross the unit cell

From: kakali sen (kakalisen_at_gmail.com)
Date: Thu Nov 25 2010 - 08:29:09 CST

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
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
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.


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