Re: Water simulation with namd

From: Binquan luan (
Date: Fri May 26 2006 - 15:09:17 CDT

You could just solvate your current water box in a bigger water box.
On Wed, 2006-05-24 at 22:32 +0100, santanu chatterjee wrote:
> Dear NAMD users,
> I am planning to simulate a box of water (with no
> less than 1000 atoms) using NAMD. I would like to use
> SPC/E water model. I have input files (PDB, PSF, PAR)
> which has 216 water molecule. Is there any way to make
> this box bigger with more water molecules with VMD
> and/or psfgen? Also, I dont know if I can generate psf
> file for water using psfgen. As far as I know, psfgen
> does not recognize any non-amino acid type of residue.
> If anybody knows any way of doing this, I will
> appreciate very much if you could share your
> knowledge.
> Santanu
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