[gmx-users] Atom ordering for RB dihedrals in OPLS-AA

prateekj prateekj at umich.edu
Fri Sep 6 20:11:46 CEST 2013


I am trying to build itp file for polymer simulations using OPLS-AA and had
two questions I could not find a clear answer from the forum or the manual.

1. Is the order of bond types listed in a row of the [dihedral] section
important, i.e. if I replace ijkl by lkji, will this make any differences.
Since type 3 is the RB dihedral, I see that the form sum_n C_n (cos(psi))^n
is unchanged with a transformation psi=-psi (or dihedral angle, phi=-phi)
but not sure. Note that I explicitly list the dihedral parameters for some
of the rows in the itp file, when the default parameters do not exist in
ffbonded.itp (in somewhat ad-hoc way for the moment by finding the closest
existing set. comments?).

2. Should I have 1-4 exclusions listed in [ pairs ] section for OPLS-AA? I
find conflicting statements when I searched on this. For example,
methanol.itp file in the OPLS-AA force-field directory lists the exclusions.


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