From: Abhishek Kumar Singh (bo13m1002_at_iith.ac.in)
Date: Tue Jan 10 2017 - 05:09:01 CST
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
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
So what can be reason for this difference. Is there any problem in this
Your suggestions are most welcome.
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