[gmx-users] Regarding Free Energy calculation tutorial

neeru sharma neeru.bioinfo at gmail.com
Thu Jun 7 14:26:10 CEST 2012

Dear Justin,

Greetings of the day!!

I am following your tutorial for the calculation of free energy change in

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?

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?

Thanks and Regards,

Neeru Sharma
CDAC, Pune, India
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