From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Mon Jul 09 2018 - 16:48:51 CDT
I am getting asymmetry in my free energy results from an ABF simulation with a ligand going from bulk water on one end of an ion channel to the the bulk water on the other side of the ion channel, which is embedded in a DMPC bilayer, and the PBC is set up so that the membrane is infinite. We expect the free energy to be essentially the same on one side of the channel as the other side. Instead, the free energy on the C-terminus bulk water side is quite lower than the free energy on the N-terminus bulk water side. Is our assumption correct the the free energies should match on both sides of the channel since the ligand is in bulk water on each side?
Kelly L. McGuire
Department of Physiology and Developmental Biology
Brigham Young University
Provo, UT 84602
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