[gmx-users] Is the discontinuity in type 2 improper dihedrals at 90 deg. or 180 deg. ?
chris.neale at alum.utoronto.ca
Sun Dec 14 03:28:29 CET 2014
In gromacs, the charmm27 force field uses type 2 (non-periodic) improper dihedrals to maintain planarity of peptide bonds.
Type 2 dihedrals are described on page 70 of the 4.6.7 manual and page 80 of the 5.0.2 manual, which contain the line (identical text):
"Since the potential is harmonic it is discontinuous, but since the discontinuity is chosen at 180 deg. distance from xi_0 this will never cause problems."
I'm a little confused about improper dihedrals, so maybe I am just not getting it, but would not the discontinuity be at +/-90 deg. (rather than 180 deg.) ? If the discontinuity were at 180 deg., then a type 2 dihedral should be able to discern between cis and trans peptide bonds, which I believe that it can not do (my interest here is eventually being able to discriminate against cis peptide bonds at very high temperatures).
Also, for type 2 improper dihedrals, isn't it the differential that is discontinuous, not the potential?
Thank you for the help,
More information about the gromacs.org_gmx-users