VMD-L Mailing List

From: Leandro Martínez (leandromartinez98_at_gmail.com)
Date: Tue Sep 23 2008 - 13:20:52 CDT

We have developed a code to do this kind of thing.
I have already suggested it to Navdeep, but maybe
it is of interest of someone else. It is GPL and available
at:

http://www.ime.unicamp.br/~martinez/packmol

With it you can build boxes of any kind of solvent and
a variety of geometries whenever you have a pdb file
of a single molecule of the solvent of interest. The boxes
are built in such a way that there are no overlaps
between atoms of different molecules, in such a way
that energy optimization or simulations run smoothly.

Hope it helps,
Leandro.

On Tue, Sep 23, 2008 at 1:32 PM, Robert Brunner <rbrunner_at_illinois.edu>wrote:

> 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
>>
>
>