[gmx-users] Dihedral angle restraints in NMR refinement...
vknecht at gwdg.de
Wed Sep 25 15:23:47 CEST 2002
> I have been playing a little bit with the NMR derived dihedral angle
> restraints as defined as impropers. I ran into the following problem:
> Dihedral angle restraints close to 180 degrees give rise to local
> heating and a lot of LINCS warnings (and exploding system).
> On page 59 of the gromacs manual it is stated that impropers should be
> defined as far away from 180 degrees as possible. The reason (dank je
> Bert!) is that the periodicity is absent and small changes in the
> dihedral angle leading to flips from ~-180 to ~+180 lead to huge
> differences in improper dihedral energy.
> So I was hoping someone of the developers-team could help us (the NMR
> users) with this.
Without extending the gromacs code, you could use periodic dihedral
restraints by defining extra proper, cosine-based dihedrals
V(phi) = k [1+cos(n phi - phi0)]
with a multiplicity
n = 1
phi0 = alpha+180
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