Re: calculating free energy

From: Aron Broom (
Date: Sat Jun 28 2014 - 15:53:02 CDT

it might help to provide what the dG actually is, it's quite subjective to
say "not reasonable", is it double expected, ten-fold what is expected?

If you choose the whole system as the receptor, you are calculating the
energy of solvating the peptide into your system out of a vacuum, that will
obviously be a lot higher than the dG of just binding to the nanotube.

On Sat, Jun 28, 2014 at 1:22 PM, Alireza Mansouri <> wrote:

> 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.

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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