Dear AMBER users,
Recently, I have done umbrella sampling for
PMF calculation using PLUMED plugin coupled with AMBER for a ligand-bound
protein. The conventional unit of spring constant is [energy units of the
program] / [units of the CV]^2. So after completing my umbrella sampling
with let's say 34 bins, we go for WHAM to generate PMF. For PLUMED, units
of the spring constant are kJ/mol/[nm]^2. Now for the calculation in WHAM,
I have to transfer units to kcal/mol/[nm]^2. For my case, I have taken the
spring constant of 300 kJ/mol/nm^2 and after conversion, the value is like
71.702 kcal/mol/nm^2. Although the WHAM program uses 0.5k(x-x0)^2, so we
have to multiply the original force constant by 2. So, the final value of
the spring constant is 143.404 kcal/mol/nm^2. After running WHAM, I am
getting the PMF values which are continuously increasing. So, am I doing
anything wrong with the unit conversion step? or there is something wrong
about tolerance value from my side (taken as 0.01) in WHAM?? Please help me
out.
thanks in advance,
Satyajit Khatua,
Dept. of Chemistry,
IIT Kharagpur,
Kharagpur-721302.
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Received on Wed Sep 18 2019 - 01:30:02 PDT
