dscerutti

In Amber the calculation for proper and improper dihedrals is indistinguishable to the engine--it all goes through the same code. In OpenMM it sounds like there is this trefoil scheme...

**Number 1** The answer is yes, 1:4 non-bonded pairs should appear in one and only one torsion, so the third atom should be negative in any other torsion that would...

**Number 2** I think that any of the torsions can indicate the 1:4 interaction. One weakness that I've always felt the Amber format has is the need to couple 1:4...

**Number 3** I think that impropers will never have 1:4 interactions, so marking the fourth atom index with a negative sign will eliminate the interactions regardless of whether the third...