Re: Simulation of a 1000 water molecules

From: Jerome Henin (
Date: Thu Aug 03 2006 - 16:35:29 CDT


You can very easily generate a waterbox and the associated topology (PSF
format) with the Solvate plugin of VMD. In VMD use the menu item
Extensions->Modeling->Add solvation box, and specify no input files, but check
the "waterbox only" box.
See a description there:


On Thursday 03 August 2006 14:19, 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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