Loss of Translational entropy calculation in FEP

From: Daniel Torrente (xlb608_at_my.utsa.edu)
Date: Wed Jul 30 2014 - 16:57:08 CDT

Dear all,

Reading the FEP tutotial in the "Binding of a potassium ion to 18-crown-6"
section they measure the the loss of translational entropy using:

−1/βln(c0∆v), where

β is equal to kB (0.001987 kcal/mol/K) * T (300 K), c0 is the standard
concentration of the ion (1mol /L=1660.6 cubic angstroms per molecule) and
∆v is the volume sampled of the ion (0.53 cubic angstroms).

In the tutorial the loss of entropy was equal to 4.8 kcal/mol but using
those values does not give me the same result. Am I overlooking an
important thing on the formula?. The standard concentration value was take
it from this post (
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2013-2014/2078.html).
I also checked other units for the c0 (mol/L) and ∆v (L) and the value of
the loss entropy is not even close.

Truly sorry for asking this type of question here.

Thanks,

Daniel
University of Texas at San Antonio

This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:21:04 CST