VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue Aug 08 2006 - 09:22:13 CDT

On 8/8/06, Vlad Cojocaru <Vlad.Cojocaru_at_eml-r.villa-bosch.de> wrote:
> Dear vmd users,
>
> Which water model is used by VMD to create waterboxes with the solvation
> plugin? Ist it TIP3P?

i didn't produce the restart, but the residue name TIP3 (in wat.pdb
in the solvate subdirectory) is a strong hint. however charmm actually
uses a slightly modified version of TIP3P that was labeled TIPS3 at
some point in time, IIRC. the geometry is the same, though.
if that difference matters to you, you have to track down the person
who originally created the restart, as the non-bonded terms needed
to distinguish those two potentials are not recorded in .psf files.

axel.

>
> Thanks
> vlad
>
> --
> Dr. Vlad Cojocaru
> EML Research gGmbH
> Molecular and Cellular Modeling Group
> Schloss-Wolfsbrunnenweg 33
> 69118 Heidelberg, Germany
> Phone: +49-6221-533266
> Fax: +49-6221-533298
> e-mail: Vlad.Cojocaru_at_eml-r.villa-bosch.de
> http://projects.villa-bosch.de/mcm/people/cojocaru/
>
>
> 

-- 
=======================================================================
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.