From: Namho Kim (namong456_at_gmail.com)
Date: Sun Jun 06 2021 - 21:18:44 CDT
Dear NAMD users
We wanted to determine free energy change upon rotation of a molecule using
'angle' colvar sampled by extended ABF but we couldn't get valuable results.
So we tested our methodology on an only-water system which consist of 251
water molecules in 20 X 20 X 20 A sized box.
In the system the center of mass of a selected water molecule was fixed at
the center of the simulation box using harmonic constraint and was only
allowed to rotate freely. We were trying to calculate the free energy
change as a function of angle between the selected water dipole and the z
axis using eABF.
It is obvious that the free energy change should be negligible with respect
to the angle because the system is isotropic. However, we obtained
unexpected result where the free energy difference is quite large (upto
~3,5 kcal/mol) and we couldn;t find any certain reason.
Below is the colvar file we used.
colvar {
name wat_fix
width 1.0
distance {
group1 {
atomnumbers { 4 5 6 } ##centered water molecule
}
group2 {
dummyAtom (0.0, 0.0, 0)
}
}
}
colvar {
name Theta
width 2.00
lowerboundary 0.0
upperboundary 180.0
extendedLagrangian on
extendedFluctuation 0.05
angle {
group1 {
atomnumbers {5 6} ##H-molecules of centered water
}
group2 {
atomnumbers {4 5 6} ##centered water molecule
}
group3 {
dummyAtom (0.0, 0.0, 1.0)
}
}
}
harmonic {
colvars wat_fix
forceConstant 10.0
centers 0.0
}
abf {
colvars Theta
fullSamples 50000
historyFreq 100
}
Thank you.
-Namho-
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