[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
> 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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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