Problem of calculating PMF changed by tilt angle using extended ABF

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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