VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri Jun 06 2008 - 09:04:27 CDT

On Fri, 6 Jun 2008, Katherine Parra wrote:

KP> Dear VMD community:
KP> I need to add a specific number of water molecules to my system (just a few
KP> of them), I tried using the solvate plugin but It is adding a large number
KP> of water molecules and I don't need a water box for my simulation.
KP> My question is: Is it possible to add a specific number of water molecules
KP> to a system without using the solvate pulgin in vmd?

katherine,

yes. see the psfgen tutorials. all that the solvate plugin does
is to create input files for psfgen. there is nothing to stop
you to superipose your system with some water molecules, check
for overlaps, write out what remains and use psfgen to build
a new topolgy.

cheers,
   axel.

KP> Thanks in advance for any help.
KP> KP
KP> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.