Re: how to add counterions ?

From: Fangqiang Zhu (
Date: Tue Dec 02 2003 - 00:24:16 CST


You have to write your own psfgen script to do this. Typical ions (e.g., Na+ or
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
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 wrote:

> Dear sir,
> I see some refenrences that when the protein is charged (not neutral) in MD
> calculation,some counterions are added to neutralize the system. Do you know how
> to do this in NAMD program?
> Thank you for your clue!

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