Tutorial-l Mailing List

From: Monika Sharma (monsharmail_at_gmail.com)
Date: Fri Jan 17 2014 - 13:27:39 CST

Hello All,

Being beginner for FEP, I tried the NAMD tutorial (
http://www.ks.uiuc.edu/Training/Tutorials/namd/FEP/tutorial-FEP.pdf), and
everything went fine. I was able to reproduce similar, comparable results.

I have one question (perhaps a stupid or naive one too!) regarding the
calculation of loss of translational entropy in the fourth section. which
is equal to
−1/βln(c0∆v), where

∆v is the effective volume sampled by the guest, which is for the potassium
ion. In the tutorial, spherical volume element of 0.52 ang^3 was
calculated for the ion. How was it calculated? Is it calculated in a
similar fashion as one calculate the surface area or is there some other
way?

For the second term c0 which is designated as the usual standard
concentration, I am confused what is meant by the standard conc, Is it like
calculating for potassium conc in the simulation box?

I know! I am stuck in the thought process, as I am missing something.
I would really appreciate it if somebody could help me out to keep going.

Thank you in advance!
Regards
Monika

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