Re: water box has a weird shape

From: Ana Celia Vila Verde (
Date: Thu Apr 07 2016 - 02:40:47 CDT

Hi Farideh,

Most likely your water box is too large for the water you have, so the
water is not uniformly distributed through out the box (i.e., you have
an "air" bubble). When these bubbles are big, it takes a while to
equilibrate them, so you're better off just restarting your simulation
with the appropriate box size.

Calculate the density of water in your simulation: you can get the final
volume from the box dimensions in the xcs file, or from the log file),
and remove the volume of the protein, if it's large (just assume it's a
sphere). If the number you get is far from 1 g/cm^3, then this is the

I hope it helps,


On 06/04/16 20:41, Aron Broom wrote:
> 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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