Re: question about free energy calculation through FEP method in NAMD

From: Ashkan Shekaari (
Date: Wed Jul 14 2021 - 05:42:02 CDT

Hi Maryam,
Give it a try using
1- SMD and then the Jarzynski's equality
2- replica-exchange umbrella sampling.
Both are implemented in NAMD.

Ashkan Shekaari
PhD Candidate in Solid State Physics
Department of Physics
K. N. Toosi University of Technology, Tehran, 15875-4416, Iran [ ] [;!!DZ3fjg!sqBe6JihE0aFs8dIlpjvF3p5aILDvQuzCcsnkUAAgrEyl9Gst96rqy7nfCWBxxkPQA$ ]

From: "M. A" <>
To: "namd-l" <>, "Jérôme Hénin" <>
Sent: Wednesday, July 14, 2021 11:05:05 AM
Subject: namd-l: question about free energy calculation through FEP method in NAMD

Dear Jérôme,

Do you have any suggestions to solve this problem?
I want to calculate the free energy ( ΔG ) between a ligand and protein through FEP method in NAMD. In my structure, the ligand is located on the surface of the protein, not inside the protein, lt means a part of the ligand that is closed to the protein surface has interaction with protein, and the other part of the ligand which is in contact with water molecules, has interaction with these molecules. So, when I change the B column of atoms of ligand to -1 (in solvate.fep file), the energy (VdW and Elc) turns off for all atoms of ligand (all atoms in contact with protein and water molecules both) while I need to eliminate the only interaction between the ligand and protein. How can I specify that it eliminates just the interaction between the ligand and protein and does not consider the interaction of ligand and water molecules.
I appreciate all your help.

best regards

Maryam Atabay 
Ph.D in Nano Computational Chemistry 
Department of Physics, Sharif University of Technology 

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