From: Jeffrey J. Potoff (jpotoff_at_chem1.eng.wayne.edu)
Date: Fri Aug 17 2007 - 08:20:28 CDT
On Fri, 17 Aug 2007, jestin mandumpal wrote:
> I am quite new to NAMD and systems that I investigate
> aqueoues DMSO, ACETONE, GLYCEROL are TREHALOSE etc.
> In order to solvate the molecule, Should I prepare
> seperate pdb, parameter and toplogy files for the
> solvent, in my case Water?
There are many different ways to do what you want. I have
students that like to call multiple topology files when building the system,
and others that like to put everything in a single file. Either way will
work fine. I do put each molecule in it's own PDB file, with is fairly easy
to do with "grep" if they are all in the same file. I like to have
everything in the same topology and parameter file, but have created my own,
since we use the TraPPE force field for many of our calculations instead
I use Packmol to generate the initial configuration, and run a short
tcl script generate the PSF file.
Jeffrey J. Potoff jpotoff_at_chem1.eng.wayne.edu
Associate Professor Wayne State University
Department of Chemical Engineering and Materials Science
5050 Anthony Wayne Dr Phone:(313)577-9357
Detroit, MI 48202 Fax: (313)578-5815
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:45:06 CST