VMD-L Mailing List

From: Robert Brunner (rbrunner_at_illinois.edu)
Date: Tue Sep 23 2008 - 11:32:42 CDT

Since I haven't seen any other replies, here's my 2 cents.

There may very well be easier or better ways to do this, but this is
how I'd proceed.

- Duplicate the molecule to fill some box with the correct density of
solvent molecules.
- Run minimization in NAMD, then some equilibration, to make a random
arrangement of the solvent molecules
- Use that as your solvent box

Robert

On Sep 19, 2008, at 4:43 PM, Navdeep wrote:

> Hi
>
> I am trying to use solvate plugin but it requires that I must have a
> cubic
> box of the solvent of choice. My question is
> 1) if I have a pdb and psf file for a single molecule of solvent, my
> case
> ethanol, how can I make a cubic box.
> 2) How to make a box of arbitrary dimensions.
>
> Is there any plugin available.
>
> Thanks
> Navdeep