[gmx-developers] site specific dH/dl

Berk Hess hess at cbr.su.se
Thu Jun 23 13:53:45 CEST 2011

Strictly speaking it is not well posed.
But in practice this might often be a useful thing to do.
You surely don't want direct interactions between the two sites.
That can be checked relatively easily. But there could also
be indirect interactions through conformational changes due
to the coupling, that is more difficult to check.

If the system here is a homo-dimer, you don't need the two numbers,
you can simply divide the total by two. But if they would couple,
this might not be correct.

But I have worked on coupling small solutes into a polymer matrix,
which often needs to be large. In that case be able to independently
couple several molecules would be very useful.


On 06/23/2011 01:37 PM, Shirts, Michael (mrs5pt) wrote:
> 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.
> Best,
> ~~~~~~~~~~~~
> Michael Shirts
> Assistant Professor
> Department of Chemical Engineering
> University of Virginia
> michael.shirts at virginia.edu
> (434)-243-1821
>> 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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