calculating free energy

From: Alireza Mansouri (
Date: Sat Jun 28 2014 - 12:22:40 CDT

Hi everybody We have a system including carbon nanotube, peptide and ions, peptide immersing water solution. We compute ∆G in this system. In this case , according to the part 4 of tutorial FEP, we choose peptide as ligand and all system (carbon nanotube , ions and water)were selected as receptor and then we computed ∆G for our system(we obtained forward and backward energy path for ligand and receptor), but according to our selection, Apparently amount of ∆G is not reasonable. What is the problem? AND is corrected choose of peptide as a ligand and all system as a receptor? Thank you.

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