From: Aron Broom (broomsday_at_gmail.com)
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 <farideh.khamseh_at_gmail.com
> 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.
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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