Re: Simulation of a 1000 water molecules

From: Neelanjana Sengupta (
Date: Thu Aug 03 2006 - 15:11:37 CDT

But that should not be a problem for you. Once the topology is specified,
you can use psfgen with your pdb file to create the required psf. This way,
it is automatically taken care of for every molecule. This should work:

topology all.rtf
segment TIP3P {
 auto none
 pdb wat.pdb
coordpdb wat401.pdb TIP3P
writepsf wat2.psf
writepdb wat2.pdb


On 8/3/06, Shenoy, Sukesh <> wrote:
> I want to generate the psf file for simulating a 1000 water molecules. The
> problem is that NAMD requires that the psf contain the bonds, angles and
> dihedral information for all the 1000 water molecules. It is cumbersome
> and
> time consuming to do this manually. Does anybody know how one can do this
> quickly (through a program perhaps)?
> Sukesh

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