[gmx-users] Calculation of dihedral force constants
Covington, Cody Lance
cody.l.covington at Vanderbilt.Edu
Fri Jun 22 15:45:07 CEST 2012
I am trying to calculate dihedral force constants from the diagonal elements in the hessian matrix in internal coordinates.
The matrix is given in hartree/rad^2. Upon conversion to kJ/(mol*rad^2) the values seem an order of magnitude higher than I have seen in the force fields (~3.77 kJ/mol for CCCH dihedral but I get ~42 kJ/(mol*rad^2). The conversion I have used is 2625.5 kJ/(mol*hartree) but is there any consideration needed for the angular units?
Another thought I had was,
The GROMACS dihedral Potential Energy function #1 (eq 4.62) listed in the manual 4.5.4 is Vd=k(1+Cos(nx-x0)) where x is dihedral angle.
so the curvature of this function (second derivative) at the minimum is (n^2)*k
so do I need to convert my force constants to this function by k_harm /n^2 = k ?
Any Help would be greatly appreciated
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