Free energy from MD Simulation

From: Nitin Bhardwaj (
Date: Wed May 31 2006 - 17:13:51 CDT

Dear NAMD users,
   I am interested in calculating the free energy between two systems
A and B. I have both these systems simulated for 1 ns using NAMD. I
know NAMD gives the total energy of the system. Is there a good paper
or way that I could refer to if I want to calculate the free energy
between these tso systems which have been simulated already? A
tutorial in this direction would also be helpful.

Any help would be greatly appreciated.

Thanks a lot

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