Re: water box has a weird shape

From: Aron Broom (
Date: Wed Apr 06 2016 - 13:41:04 CDT

you should first search the mailing list about weird water box shapes.
This is a very common visualization problem (nothing wrong with the actual
simulation) related to the wrapping of atom coordinates around your
periodic boundary conditions.

I can't recall the details, but I know there are many threads out there
that will likely give advice for fixing the issue or maybe reveal that
there really is a problem.

On Wed, Apr 6, 2016 at 2:21 PM, faride badalkhani <
> wrote:

> Hi,
> I run a NPT simulation but when I load the trajectory file in VMD the
> water box has a strange shape (something like a saddle). Could you tell me
> what is the reason?
> Any help will be appreciated.
> Regards,
> Farideh

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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