**From:** Monika Sharma (*monsharmail_at_gmail.com*)

**Date:** Sun Jan 19 2014 - 11:32:02 CST

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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

**Next message:**James Starlight: "Reassure fluctuations in course of simulation"**Previous message:**Vidhya Sankar: "About Psfgen error for Lipid molecules"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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