[gmx-developers] Re: site specific dH/dl

Lishan Yao yaolisha at msu.edu
Thu Jun 23 13:52:27 CEST 2011

Hi Berk,
   Thank you for the response. I will do it in the easy way first by defining some kind of groups and then write out dH/dl for each group. But I don't know which code file I need to change (not familiar with Gromacs code). Once I have dH/dl, I can do the integration using traditional TI (will worry about Bennett later). 


> Message: 3
> Date: Thu, 23 Jun 2011 11:47:06 +0800
> From: "Lishan Yao" <yaolisha at msu.edu>
> Subject: [gmx-developers] site specific dH/dl
> To: <gmx-developers at gromacs.org>
> Message-ID: <E49D19F64EBE4EAB86DC7C8C286880F6 at lenovo282d43b3>
> Content-Type: text/plain; charset="iso-8859-1"
> 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
> ------------------------------
> Message: 4
> Date: Thu, 23 Jun 2011 11:26:49 +0200
> From: Berk Hess <hess at cbr.su.se>
> Subject: Re: [gmx-developers] site specific dH/dl
> To: Discussion list for GROMACS development
> <gmx-developers at gromacs.org>
> Message-ID: <4E0306D9.3030909 at cbr.su.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 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

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