From: Monika Sharma (monsharmail_at_gmail.com)
Date: Tue Feb 04 2014 - 14:05:49 CST
Dear NAMD users,
Being beginner for FEP, I tried the NAMD tutorial (
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
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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