From: Axel Kohlmeyer (
Date: Thu Jul 26 2007 - 11:41:04 CDT

On Thu, 26 Jul 2007, Vijaya Brahma wrote:

VB> Dear ALL
VB> I am using VMD 1.8.5 in the Linux version 2.6.9-5.ELsmp.I have solvated my
VB> protein in a water box giving the PDB and PSF input with the boundary of
VB> 2.8 and the box size using the molecules' dimension itself without box
VB> padding .
VB> I am having this unique problem, I need a water box size such that it is
VB> only and strictly 8 Ang. away from any side of the molecule. Is it
VB> possible in VMD?? Please let me know the script for the same.

well, strictly 8 angstrom away from a protein is actually not that
well defined. you can try to take the water box that you created from
the solvation and then build an atom selection that contains only
the atoms/waters, that interest you and build an updated topology
with psfgen. please keep in mind that the solvate package leaves
some safety around your peptide and that you'll probably first have
to relax the bulk system, for a while to get what you need (and even
then you have to expect that the water density at the surface of
your water hull is going down during equilibration, leading to a
larger diameter of the hull).


VB> Thanks and Regards,

Axel Kohlmeyer
   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.