Re: [AMBER] Thermodynamic Integration introduce charge

From: Ignacio J. General <ijgeneral.gmail.com>
Date: Wed, 4 May 2016 08:15:35 -0300

Hi. As Hannes says, you can do it, but you should be really careful. The
main problem is that when you introduce a charge, the Ewald summation that
Amber does will automatically (and implicitly) introduce a counter charge,
in order to neutralize the system (since Ewald is not defined for
non-neutral systems). Thus, the free energy you get after doing this is not
the free energy of introducing your charge, but will also include the free
energy for the introduction of that other neutralizing charge.



On Wed, May 4, 2016 at 3:10 AM, <hannes.loeffler.stfc.ac.uk> wrote:

> Technically possible, yes but you should consult the literature (PH
> H├╝nenberger is a good place to start from) to see what this entails and
> what correction for artefacts have been used.
> ________________________________________
> From: Johannes Loeffler [johannes.r.loeffler.gmail.com]
> Sent: 04 May 2016 06:36
> To: AMBER Mailing List
> Subject: [AMBER] Thermodynamic Integration introduce charge
>
> Dear all,
>
> Is it possible to perform thermodynamic integration if the point
> mutation includes introducing a charge?
>
> Thanks in advance!
>
> Joe
>
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Received on Wed May 04 2016 - 04:30:05 PDT
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