[gmx-users] Regarding Free Energy calculation tutorial

Justin A. Lemkul jalemkul at vt.edu
Thu Jun 7 14:53:22 CEST 2012

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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