**From:** Abhishek Kumar Singh (*bo13m1002_at_iith.ac.in*)

**Date:** Tue Jan 10 2017 - 05:09:01 CST

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Hello,

I have alchemically transformed K+ to Na+ at the center of water boxes (40,

60 and 80 A edge length respectively) using NAMD software and CHARMM36

forcefield. A harmonic spring of force constant = 10 kcal/mol.A^-2 has been

applied throughout the transformation. Temp and Pressure has been kept at

310K and 1 atm respectively.

Free energy of alchemical transformation has been calculated using

thermodynamic integaration. The derivative has been computed as (∂G/∂λ) = ⟨

U(λ=1)- U)(λ=0) ⟩λ, where λ is the coupling parameter such that λ=1 and λ=0

are K+ and Na+ vdw parameters respectively. Free energy derivatives has

been computed for 11 λvdw values ( 1.0, 0.9, 0.8, 0.7, 0.6, 0.5, 0.4, 0.3,

0.2, 0.1 and 0.0). The area under the plot (derivate vs λ) gives me = -23.40,

-23.46 and -23.4

8

kcal/mol for the box sizes of 40A, 60A and 80A respectively. I am

attaching alongwith the derivate vsλ values for 40A water box.

The standard CHARMM36 prm file actually states that the value should be

-18.6 kcal/mol.

So what can be reason for this difference. Is there any problem in this

procedure ?

Your suggestions are most welcome.

Sincerely

Abhishek

- application/octet-stream attachment: derivate_vs___values

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