[gmx-developers] site specific dH/dl

Shirts, Michael (mrs5pt) mrs5pt at eservices.virginia.edu
Thu Jun 23 13:37:15 CEST 2011

I'm not sure the question is even well-posed.  If you change two things at
once, you cannot decompose what the free energy is into two spatially
separate parts.  You can compute the free energy of the first mutation, then
performing the second mutation given that the first mutation exists.  Both
free energies will be different (perhaps not very different if the locations
as well separated) than if you tried to do both at once.

Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu

> From: Berk Hess <hess at cbr.su.se>
> Reply-To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
> Date: Thu, 23 Jun 2011 11:26:49 +0200
> To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
> Subject: Re: [gmx-developers] site specific dH/dl
> Hi,
> This is impossible with the current code.
> It would not be too hard to this with the Bennett's acceptance ratio code,
> but that requires the code as well as the analysis tools to support multiple
> decoupling groups (which could be done through energy groups).
> This is mainly a bookkeeping issue, which would also require a change
> of file formats.
> Berk
> On 06/23/2011 05:47 AM, Lishan Yao wrote:
>> Hi:
>> I did a MD TI simulation for a T->  A mutation in a protein dimer. The
>> mutations were done in both sites simultaneously. My question is how can I
>> extract dH/dl for each T->A site. Gromacs gives the total dH/dl. Which part
>> of the code should I change?
>> Best,
>> Lishan
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