From: Axel Kohlmeyer (
Date: Sat Jun 05 2010 - 19:32:54 CDT

On Sat, Jun 5, 2010 at 7:31 PM, David Li <> wrote:
> Dear all,
> I want to add water box to my studied protein by VMD solvate plugin. I
> noticed that the generated water box by VMD is based on a smaller
> water box pdb file located in
> ${VMD_path}/lib/vmd/plugins/noarch/tcl/solvate1.2/wat.pdb. Does anybody know
> the the size of this wat.pdb and the desity of this water box?

the box is cubic with 65.4195 side length. density should be around
1.0 g/l, but that is mostly irrelevant. after solvation you will have to
shrink your initial cell to the proper density in any case.

> Why the water number is 9261 and why the solvate plugin starts from this
> water box?

21*21*21 = 9261

why not use this box??


> Any clue is appreciated.
> Ardie

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.