VMD-L Mailing List

From: David Li (vmd.reading_at_googlemail.com)
Date: Wed Jun 09 2010 - 05:33:10 CDT

Dear Dr. Axel Kohlmeyer,
Thanks for your quick reply. I don't doubt about the validity of the water
box but just want to know the very basic information about it.
Could you please give me more instruction? I mean if I want to build such a
water box, what should I start from?

Thank you.

Ardie

2010/6/6 Axel Kohlmeyer <akohlmey_at_gmail.com>

> On Sat, Jun 5, 2010 at 7:31 PM, David Li <vmd.reading_at_googlemail.com>
> 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??
>
> cheers,
> axel.
>
> >
> > Any clue is appreciated.
> >
> > Ardie
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> http://sites.google.com/site/akohlmey/
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>