Re: how to add counterions ?

From: Fangqiang Zhu (
Date: Tue Dec 02 2003 - 18:19:19 CST

You don't have to know the exact coordinates of bulk water molecules. You only
need to roughly know the bulk water region, and place your ions at whatever
positions in that region. If you like, of course you can also solvate your system
and then add your ions.

Zhu, Fangqiang wrote:

> Dear Fangqiang Zhu,
> Thank you for your reply!
> I am sorry I don't understand the sentence"you may simply place them randomly in
> bulk water". Before I solvate the protein, I don't know the coordinates of water.
> How should I put ion in bulk water? Maybe I should first solvate the protein, then
> I can get the coordinate of water( for example: 1.0,1.0,1.0), so I add coordinate
> (1.5,1.5,1.5) to ion in the pdb file of ion. Is my method right?
> >From: Fangqiang Zhu <>
> >Reply-To:
> >To:
> >Subject: Re: namd-l: how to add counterions ?
> >
> >Hi,
> >
> > You have to write your own psfgen script to do this. Typical ions (e.g., Na+ or
> > Cl-)
> > are already defined in the CHARMM topology and parameter files, so what you
> > need to do is to, e.g., create a new segment and add ions to this segment. As
> for
> > the
> > coordinates of the ions, you may simply place them randomly in bulk water.
> > Remember to minimize your system before starting the real simulation, because
> > there may be bad contact between ions and water molecules.
> >
> > Zhu, Fangqiang

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