Re: [AMBER] Is the neutralization necessary for the GB model?

From: Jason Swails <>
Date: Mon, 7 Mar 2011 13:42:07 -0800


>From a quick glance at the tutorial, it appears as though that was just
there as a demonstration there to show you where ions are added to the
system. If you look carefully at the simulations that are being run in that
tutorial, the vacuum (and GB) simulations do *not* use the counter ion

You should not add counter ions if you want to simulate in GB -- simply add
a saltcon to account for electrostatic screening by a set ionic strength.
Read the tutorial carefully as it describes in detail what simulations are
being run and what we learn from them.

Hope this helps,

On Mon, Mar 7, 2011 at 1:24 PM, zhihong ke <> wrote:

> Dear All,
> Is the neutralization necessary for the GB model? In the tutorial B1, it is
> suggested to neutralize the system for the implicit water model. If so, a
> neutral system should be used to run REMD simulations, correct?
> Any help would be appreciated!
> Regards,
> Zhihong
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Mon Mar 07 2011 - 14:00:04 PST
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