Re: Water simulation with namd

From: Peter Freddolino (
Date: Wed May 24 2006 - 17:45:30 CDT

Hi Santanu,
psfgen certainly can recognize non-protein residues; you just need to
make sure that whatever waters you do have in your system are in your
topology file.
As far as making the box bigger, your best bet is probably to use vmd to
move the box around and write several different pdb files, and then
consider each of those files a chain for psfgen. For example, you could
do a 2x2x2 tiling by doing something like

set sel [atomselect top all]
$sel writepdb chain1.pdb
$sel moveby {a 0 0}
$sel writepdb chain2.pdb
$sel moveby {-a b 0}
$sel writepdb chain3.pdb

(with a, b the x and y lengths of your water cell). This part can also
be automated. I'd note that you can also use the vmd solvate plugin to
create a water box of arbitrary size, and then just change the residue
name of the waters to (say) SPC (if that's what you have in your
topology file).


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
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