VMD-L Mailing List
From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Jun 05 2010 - 19:32:54 CDT
- Next message: Reid Van Lehn: "Re: Trouble compiling from source - Mac OS X"
- Previous message: David Li: "about vmd solvation plugin"
- In reply to: David Li: "about vmd solvation plugin"
- Next in thread: David Li: "Re: about vmd solvation plugin"
- Reply: David Li: "Re: about vmd solvation plugin"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
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.
- Next message: Reid Van Lehn: "Re: Trouble compiling from source - Mac OS X"
- Previous message: David Li: "about vmd solvation plugin"
- In reply to: David Li: "about vmd solvation plugin"
- Next in thread: David Li: "Re: about vmd solvation plugin"
- Reply: David Li: "Re: about vmd solvation plugin"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]