Hello everyone,
I am planning to run a classical simulation (amber99sb-ildn.ff) in which I need to scale the nonbonded interactions between two atoms. In further steps, I may want to expand the set of atoms for which this condition should hold. I’m not quite sure how to approach this. My current idea is to first exclude the atoms using the [exclusions] directive, and then add the Coulombic (QQ) and Lennard-Jones (LJ) interactions using the [pairs] directive. I would like to set different fudge factors for these atoms, but I’m not quite sure how the function types in the [pairs] directive work. According to my understanding, I need to use function type 2, but I am unclear about the required parameters. The manual describes them in the following way: fudge QQ (); qi; qj (e), V ; W. (Could someone please elaborate? How many parameters are there?)
My main concern is whether I can assign both fudge factors directly (what i prefer) in the [pairs] directive or if I need to provide scaled force field parameters by myself. I’m quite confused about this aspect. If anyone could provide some insights or explanations on this matter, it would be greatly appreciated.
Thank you in advance for your help!
Best regards,
Julian