AMBER Archive (2006)

Subject: Re: AMBER: Ti calculations in dmso solvent

From: David Mobley (dmobley_at_gmail.com)
Date: Thu Feb 23 2006 - 14:06:43 CST

Dear Dr. Case,

This subject has been carefully explored here:
>
> %A T. Darden
> %A D. Pearlman
> %A L.G. Pedersen
> %T Ionic charging free energies: Spherical versus periodic boundary
> conditions
> %J J. Chem. Phys.
> %V 109
> %P 10921-10935
> %D 1998
>
> This paper argues that you can do standard charging free energy
> calculations
> in a straightforward fashion using PME. There is no requirement in PME
> that
> the system be neutral...indeed, it can't be at both ends of a charge
> change. As
> my comment, I don't see how using cutoff electrostatics would lead to
> consistent or correct results.

Great, thanks for the reference. I'd been asking people about this but
couldn't find anyone who knew whether it would really work properly or not,
or what the relevant references were...

Thanks!
David

For a recent application of free energy calculations where the charge is
> changing, you might look here (among other places!):
>
> %A T. Simonson
> %A J. Carlsson
> %A D.A. Case
> %T Proton binding to proteins: pKa calculations with explicit and implicit
> solvent models
> %J J. Am. Chem. Soc.
> %V 126
> %P 4167-4180
> %D 2004
>
> ....dac
>
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