[gmx-users] Regarding Free Energy calculation tutorial

[Justin A. Lemkul]

On 6/7/12 8:26 AM, neeru sharma wrote:
> Dear Justin,
>
> Greetings of the day!!
>
> I am following your tutorial for the calculation of free energy change in gromacs.
>
> It says about the change in state A and state B. I have a query regarding these
> states. What are the 2 states A and B in the tutorial and how can I define these
> 2 states for my system?
>

The changes applied between state A and B are defined in the .mdp file based on 
the couple-lambda0 and couple-lambda1 settings.  These are used to transform 
either vdW or Coulombic interactions.  If you need to make some other type of 
change (i.e. a mutation), then you would do so in the topology, setting B-state 
parameters explicitly.

> For example, I have a Protein-Mg-GTP complex (In initial state A, 2 specific
> H-bonds are absent and in the final state, these 2 H-bonds are present). So, how
> can I implement this for the calculation of change in free energy to my system?
>

This doesn't sound like something that can be done with the decoupling 
technique; it sounds to me more like a structural change.  Perhaps you can do 
some careful calculations using the pull code, but it is not clear to me what 
you are trying to do.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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