From: Faisal, H M Nasrullah (
Date: Tue Dec 22 2020 - 20:52:34 CST

Dear JC,

Thanks for your kind reply. I totally overlooked that matter.


From: Gumbart, JC <>
Sent: Tuesday, December 22, 2020 8:43 PM
To: <>; Faisal, H M Nasrullah <>
Cc: <>; <>
Subject: Re: namd-l: Query regarding 'Protein:ligand Standard Binding Free Energies' tutorial

Good question. In fact, that file (bound.fep) is not used at all from what I can tell. For determining the role of the restraints, the alchemical route uses thermodynamic integration through colvars.


On Dec 22, 2020, at 3:39 PM, Faisal, H M Nasrullah <<>> wrote:

Dear all,

I am trying to go through the tutorial of Standard Binding Free Energies between protein and Ligand. I am a bit confused regarding the 'bound.fep' file from 'Restraints%3ABound' directory under the 'AlchemicalRoute' archives. My question is why the protein was being decoupled from the system instead of the ligand (the beta column of protein is tagged with -1)? Can anybody please give me some insight?

Thanks in advance.