AMBER Archive (2006)

Subject: Re: AMBER: Periodic simulations with net charge

From: David A. Case (case_at_scripps.edu)
Date: Tue Nov 28 2006 - 20:03:22 CST

On Tue, Nov 28, 2006, Jennie Thomas wrote:
>
> I am looking for some advice as to how to run a periodic system with
> a net charge within the box of -1. Looking at some old mailing list
> information, I found the following suggestion:
>
> http://structbio.vanderbilt.edu/archives/amber-archive/2000/0470.php
>

As you note, that message refers to old versions of Amber. Both Amber8
and Amber9 "do the right thing" (tm): if there is a net charge, then a
neutralizing background is automagically added. User input is no different
for a neutral system than for a charged system.

....regards...dac

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