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

From: M. A (matabay2010_at_gmail.com)
Date: Wed Jul 14 2021 - 14:40:56 CDT

Dear Ashkan,
Hi
Thank you for your help. Both methods you recommended are time-consuming
and I have no enough time and in addition, the FEP method worked for my
other simulations except for the problem that I mentioned I didn't have any
problems with.

bests,
Maryam

On Wed, Jul 14, 2021 at 3:12 PM Ashkan Shekaari <shekaari_at_email.kntu.ac.ir>
wrote:

> Hi Maryam,
> Give it a try using
> 1- SMD and then the Jarzynski's equality
> or
> 2- replica-exchange umbrella sampling.
> Both are implemented in NAMD.
>
> ---
> ,Best
> Ashkan Shekaari
> PhD Candidate in Solid State Physics
> Department of Physics
> K. N. Toosi University of Technology, Tehran, 15875-4416, Iran
> <shekaari_at_email.kntu.ac.ir>
>
> ------------------------------
> *From: *"M. A" <matabay2010_at_gmail.com>
> *To: *"namd-l" <namd-l_at_ks.uiuc.edu>, "Jérôme Hénin" <jerome.henin_at_ibpc.fr>
> *Sent: *Wednesday, July 14, 2021 11:05:05 AM
> *Subject: *namd-l: question about free energy calculation through FEP
> method in NAMD
>
> Dear Jérôme,
> Hi
>
> 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
>
> --
> Maryam Atabay
> Ph.D in Nano Computational Chemistry
> Department of Physics, Sharif University of Technology
>
>
>

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

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