Re: Re: deformed water box during equilibration.

From: Neelanjana Sengupta (
Date: Sat Oct 21 2006 - 14:26:17 CDT

Hi Dhiraj,

> I was equilibrating my protein solvated in water box. after several
> times of restarting the simulation, i found that the box is looking
> deformed. but number of atoms in the system was same as before.
> >
> > What may be the reason for this? do i need to update cell basis vectors
> > and origin of "periodic boundary condition" every time i restart the
> > simulation?
> >
> ***********************
It is only natural for your water molecules to diffuse out as time goes, and
when you visualizing this gives you the impression that your box is getting
'deformed'. In reality, if periodic boundary conditions apply, you have
mirror images of the molecules, and the force will be due to molecules on
all sides.

If you want to maintain the shape of your box, use the option "wrapAll on".


Neelanjana Sengupta, PhD student
Dept. of Chemistry
Univ. of California-Irvine
Irvine, CA 92697
Phone: 1-949-824 9921

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