[gmx-users] Why is there a difference between an angle of 0 or 180 deg. for a type 9 proper dihedral with multiplicity of 2?

Justin Lemkul jalemkul at vt.edu
Sat Jul 4 15:41:37 CEST 2015

On 7/4/15 3:32 AM, Christopher Neale wrote:
> Dear Gromacs users:
> I have been working on creating a topology for an exotic molecule. It
> contains aromatic rings and my parameters always seemed to allow the rings to
> buckle and become non-planer, much like a glucose ring would (though a little
> less extensively). However, I have managed to solve the problem by switching
> my proper (type 9) dihedral angles from angle = 0 degrees, multiplicity = 2
> to angle = 180 degrees, multiplicity = 2. I thought that those two conditions
> should be equivalent and it was only by seriously simplifying the molecule
> down to a single ring and then toying with every conceivable parameter that I
> even hit on this. I am using gromacs 4.6.3 and have not tried other versions
> of gromacs, but this makes so little sense to me that I thought I would ask
> about it here. There are lots of proper dihedrals in the available force
> fields that use dihedrals with a set angle of zero degrees, though I do note
> that for any aromatic ring that I have seen they are always 180 deg (with
> mul tiplicity of 2 so that they can handle both cis and trans). Presumably I
> have just missed some obvious definition, but at least I can verify that if I
> switch even one proper dihedral from angle = 180 back to angle = 0 (with
> multiplicity = 2 in each case), then I start to see deformation of the ring's
> planarity.

Some deformation is not necessarily unphysical.  Aromatic rings in CHARMM are 
treated like this, for instance.  It shouldn't be substantial, but it shouldn't 
remain exactly planar, either.  What are the parameters you're using?  The 
choice of 0 vs. 180 here for multiplicity = 2 should indeed be irrelevant.  Have 
you gone down to something as simple as, e.g. benzene?



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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