Re: Simulation of a 1000 water molecules

From: L. Michel Espinoza-Fonseca (
Date: Thu Aug 03 2006 - 14:34:47 CDT

When you say that NAMD requires "bond, angle and dihedral information"
you mean that you need NAMD requires de topology, isn't it? In
principle if you want to simulate a system containing 1000 water
molecules, you'll need only the bond and angle information. You can
easily get the topology (as a pdb file) and parameters (all the rest)
by using psfgen, which is included in both NAMD and VMD. You don't
need to do this by hand. If I didn't understand you well, pls make me
know :)


2006/8/3, Shenoy, Sukesh <>:
> 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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