From: Sunhwan Jo (sunhwan_at_uchicago.edu)
Date: Tue Feb 04 2014 - 14:47:17 CST
If you have a look at the first paragraph and page 35, you can find a sentence saying,
Here, a confinement potential will be imposed on the ion to remain within a sphere of 1 A ̊ diameter.
Thus, dv = 4/3 * pi * 0.5^3 = 0.52..
On Feb 4, 2014, at 2:05 PM, Monika Sharma <monsharmail_at_gmail.com<mailto:monsharmail_at_gmail.com>> wrote:
Dear NAMD users,
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
∆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!
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