On 22/06/2012 11:45 PM, Covington, Cody Lance wrote:
Dear gmx-users
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 ?
You should really be looking at the literature for the force field you
are trying to extend or emulate, and see what data and method they used
to fit these values. The GROMACS documentation is of necessity generic.
Some force fields have a scaled 1,4 electrostatic interaction that will
vary with the dihedral angle. There can be multiple dihedral angle
functions around a single bond and these may add together.
Mark
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