[gmx-users] Solvating a non-orthogonal box

Dallas Warren dallas.warren at monash.edu
Tue May 15 00:08:48 CEST 2018

This isn't a PBC issue with visualising the box, is it?  Turn on the
neighbouring images when visualising, and you will be able to see
quickly if the entire space is actually filled or not.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
When the only tool you own is a hammer, every problem begins to resemble a nail.

On 15 May 2018 at 05:21, Anuradha Bhat <anur.bhat at gmail.com> wrote:
> Hi
> I have a box whose vectors are given by:
>   (7.97262    0.00000   0.00000),  (-0.96054   2.33646  0.00000),
> (15.00000          0.00000   0.00000). I would like to fill this box with
> water. When I use gmx solvate to fill this box, it seems to be introducing
> a rectangular shaped box of water, rather than a box of the desired shape.
> Therefore, water does not fill the entirety of the box. Is there a way to
> fill a non-orthogonal shaped box with the solvate command?
> Thanks in advance,
> Annu.
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