Re: how to add counterions ?

Date: Tue Dec 02 2003 - 01:54:09 CST

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 <>
>Subject: Re: namd-l: how to add counterions ?
> 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
> 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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