From: Jérôme Hénin (
Date: Thu Oct 06 2011 - 06:15:48 CDT

Hi Leandro,

You can first generate a large cubic box that contains the hexagonal
cell, and then save only the molecules that are inside the hexagonal
cell using selection texts dependent on coordinates, like "2 * x + 3 *
y < 0" etc.

Best wishes,

On 5 October 2011 20:00, Leandro Barros da Silva
<> wrote:
> Hi users,
> I'm interested in study a system with PBC using an hexagonal cell. I'm
> trying to use VMD solvate script to add water molecules to the cell, but
> this only generates (as far as I know) cubic/parallelepipidic cell. Any
> hints on how to solvate (and generate the corresponding NAMD topoplogies)
> cells with shapes other than cubic?
> Best wishes and thanks in advance!
> Leandro B da Silva