Re: deformed water box during equilibration.

From: Leandro Martínez (
Date: Sat Oct 21 2006 - 10:45:09 CDT

Deformed how? Are you using periodic boundary conditions? A square
box of water will become somewhat spheric if you are not using periodic
boundary conditions. Furthermore, if you are using them you need
to use the wrapall option to the coordinates in the output file
contain the images in the actual box.

Leandro Martinez
State University of Campinas, Brasil

On 10/21/06, Dhiraj Srivastava <> wrote:
> Hi all
> 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? i have restarted the simulation almost 8 or 9 times.
> Thank you for help.
> --
> Dhiraj Kumar Srivastava
> Department of Chemistry
> University of Missouri-Columbia
> MO, 65211

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