hello, I am using the obenergy program and GAFF force field to compute the
potential energy of some molecule, according to the following program
example:
obenergy -ff GAFF
/Users/Eric/Desktop/ExampleMolecules/GAFF-test-set/21208702.mol
according to forcefieldgaff.cpp, the energy is given by the sum of the
following components:
energy = kr * delta;
energy = kth * delta2;
energy = vn_half * phi1;//torsion
energy = vn_half * phi1;//out of plane bending
energy = Eab * (term12 - 2.0*term6);
energy = qq / rab;
Where are kr, kth, vn_half, etc. defined? They don't seem to be explicitly
stated in the gaff.dat file. For example, kr is defined as
bondcalc.kr = KCAL_TO_KJ * parameter->_dpar[0];
Can someone explain what _dpar[0]? I surmise that it references a number in
gaff.dat in some fashion though I'm not sure how. All I need to know is
which number _dpar[0] corresponds to in the .dat file, and how this
correspondence is achieved.
Thanks!
- Eric
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