Re: Question regarding loss of translational entropy calculation in FEP tutorial

From: Aron Broom (
Date: Tue Feb 04 2014 - 14:22:31 CST

c0 is the standard concentration at which you'd want to calculate dG. The
standard concentration is generally 1M, but the value of that constant
should be in cubic angstroms or something volume related. So I think it is
calculated as 1 L / Na (avagadro's number), and thus, is the volume
allotted to each ligand molecule when at standard concentration. 1 L is 10
cm cubic box, so it would be 1x10^27 cubic Angstroms. So 1x10^27 /
6.022x10^23 is 1660.6 cubic angstroms per molecule, and I think that 1660.6
is what c0 is generally entered as.

I don't know about the other volume, you might look at what the VDW radius
is for that ion, and then calculate the volume of the sphere, maybe that
will be close.

On Tue, Feb 4, 2014 at 3:05 PM, Monika Sharma <> wrote:

> Dear NAMD users,
> Being beginner for FEP, I tried the NAMD tutorial (
>, and
> everything went fine. I was able to reproduce similar, comparable results--047d7bf10a845b25a604f19a663d--

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