From: esmael (haddadian_at_uchicago.edu)
Date: Fri Jul 22 2011 - 19:10:59 CDT
I am trying to calculate the free energy of charging two spherical particles in water fixed at a given distance using the FEP within NAMD. These two particles are not bonded; should I set the "alchDecouple" to on or off? I would like that these two particles "see" each other and interact during the course of FEP calculations (and the interaction energy be included in the total free energy).
Thanks a lot,
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