AMBER Archive (2002)

Subject: Re: counter-ions in FEP

From: David A. Case (case_at_scripps.edu)
Date: Fri Jul 12 2002 - 11:00:11 CDT

On Thu, Jul 11, 2002, Christophe L M J Verlinde wrote:

> I would like an opinion on the following FEP simulation:
> My protein has a net charge of +3. In my simulations
> with explicit TIP3P water I usually add counterions to
> obtain a neutral system. However, now I am faced with
> performing a FEP simulation in which a neutral ligand
> is changed into an isosteric ligand with net charge -1.
> Should I keep the system neutral in both states of the FEP?
>

This is neither possible nor desirable in calculating "charging free
energies" (where the system charge is changing.) See, e.g.
Darden, Pearlman and Pedersen, J Chem Phys 109: 10921 (1998). In
general, it is best to use a method like Ewald or PME for these
sorts of calculations, since the long-range electrostatic contributions
can be significant.

..hope this helps...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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