Re: how to add counterions ?

From: Alessandro Pedretti (
Date: Tue Dec 02 2003 - 06:18:58 CST

You can place the counterions with Sodium software
( or if you are using a
Windows system, you can do it with VEGA OpenGL ( It
implements the same routines developed by Alexander Balaeff expanded to use
different counterions and to neutralize the macromolecules. All these
functions are accessible thanks to the VEGA graphic interface. These
routines are interesting because the ions aren't palced randomly but in the
nodes of a cubic grid in which the electrostatic energy achieves the
smallest values.

        Alessandro Pedretti

----- Original Message -----
From: <>
To: <>
Sent: Sunday, November 30, 2003 11:59 AM
Subject: namd-l: how to add counterions ?

> Dear sir,
> I see some refenrences that when the protein is charged (not neutral) in
> 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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