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Message: 1<br>
Date: Thu, 07 Jun 2012 08:53:22 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] Regarding Free Energy calculation tutorial<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4FD0A442.6000107@vt.edu">4FD0A442.6000107@vt.edu</a>><br>
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On 6/7/12 8:26 AM, neeru sharma wrote:<br>
> Dear Justin,<br>
><br>
> Greetings of the day!!<br>
><br>
> I am following your tutorial for the calculation of free energy change in gromacs.<br>
><br>
> It says about the change in state A and state B. I have a query regarding these<br>
> states. What are the 2 states A and B in the tutorial and how can I define these<br>
> 2 states for my system?<br>
><br>
<br>
The changes applied between state A and B are defined in the .mdp file based on<br>
the couple-lambda0 and couple-lambda1 settings. These are used to transform<br>
either vdW or Coulombic interactions. If you need to make some other type of<br>
change (i.e. a mutation), then you would do so in the topology, setting B-state<br>
parameters explicitly.<br>
<br>
> For example, I have a Protein-Mg-GTP complex (In initial state A, 2 specific<br>
> H-bonds are absent and in the final state, these 2 H-bonds are present). So, how<br>
> can I implement this for the calculation of change in free energy to my system?<br>
><br>
<br>
This doesn't sound like something that can be done with the decoupling<br>
technique; it sounds to me more like a structural change. Perhaps you can do<br>
some careful calculations using the pull code, but it is not clear to me what<br>
you are trying to do.<br>
<br>
-Justin<br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul, Ph.D.<br>
Research Scientist<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
</blockquote></div><br>Thanks for the reply. <br>Well,yes it is more of the strutural change in case of my case which can also be quantified in terms of presence and absence of these 2 H-bonds. And as the two structures are distinct from each other too, there has to be some energy change which I want to calculate too. Moreover, this structure change and the appearance of these H-bonds take long time and cross a energetic barrier too, I am trying to calculate this energy barrier too.<br>
Regarding the pull code, I will also try it for my system<br><br>---<br>Neeru<br><br>