Hi all,
I’m slightly lost on the description of the RB and Fourier potentials for proper dihedrals as described in the below link:
In equation (200) the Fourier potential is given with parameters F1 to F4, which is then converted into the RB parameters via equation (201). The RB parameters are called C0 to C4. Then, in equation (202) the Fourier potential is given again but this time the parameters are C1, C2, C3 and C4. To me this is implying that to use the Fourier potential with option 5 in the topology file I have to convert the F1, F2 and F3 into Cs with equations (201) and then use C1, C2, C3 and C4 in the topology file. I don’t think I understand why this is.
The OPLS/AA CT-CT-CT-HC dihedral is 0.0 0.0 0.3 0.0. I assumed all I would have to do here is make the kcal/mol to kJ/mol conversion to use topology option 5, but do I have to make a more complicated conversion?
Thanks