I was trying to understand how the GAFF force field was defined in the gaff.lib file (at gulp-6.1.2/Libraries/).
Two questions came up:
why in the section “epsilon kcal” every sigma (in fact r_min) value is multiplied by 2?
Amber uses the r_min notation, which is the same used by GULP once “lennard epsilon geometric 12 6 x13 kcal all 0.5 12.0” is defined.
I don’t understand this explanation:
“# NNB: In Amber one of two improper torsions is chosen whereas in GULP both improper angles are used but the force constant is halved.”
I was looking in both AMBER and GULP manuals and could not find the reason for dividing by 2 the force constant of the improper torsions.
Dear Alexa,
The difference in the sigmas is probably just because GULP’s combination rules takes the average of the sigma for each element (sigma_i + sigma_j)/2, whereas I suspect AMBER may include the factor of a half in the sigma so that they just get added.
For improper torsions, some codes just use 1 of several possible improper torsion angles for a set of atoms, whereas GULP will take all combinations that satisfy the criteria specified. Therefore to match the behaviour of other codes it’s necessary to divided by the multiplicity of the improper torsions.
Regards,
Julian