I’m using force field parameters from a paper, building the top file in gromacs. I’m a bit stuck on the concept of multiplicity for improper dihedrals.
My questions are:
What does multiplicity mean in the context of improper dihedrals?
How do I choose the right multiplicity number for any dihedral? Any explaintion or links would be really helpful!
Hi Yehonatan you can scan the below link starting at the bottom of page 30 into the illustration on page 33, the multiplicity (periodicity) is exhibited in this ffTK Tutorial.
A quote from the link:
`For very simple molecular geometries such terms can be determined by chemical intuition; however, it is also a good strategy to find analogous molecules (or functional groups) in the standard CGenFF distribution to obtain more information regarding dihedral terms for specific connectivities.´
Possible conformation of a molecule compared to their energies, you may need to just juggle different conformations via intuition and or create a .prm or .par file which will exhibit these eg. below of a .prm file (you can create this via ffTK or I believe Gromacs and or CGenFF.