[gmx-users] Is the discontinuity in type 2 improper dihedrals at 90 deg. or 180 deg. ?

[Justin Lemkul]

On 12/13/14 9:28 PM, Christopher Neale wrote:
> Dear Users:
>
> 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).
>

Isn't this an issue of proper dihedrals, not impropers?  A cis-trans 
isomerization involves an actual bond rotation about C-N; that's not what the 
impropers are acting on.  If this were related to improper terms, you'd have 
C-N-CA in the same plane, but the H bending over backwards into something 
totally non-physical.

> Also, for type 2 improper dihedrals, isn't it the differential that is discontinuous, not the potential?
>

The nature of the discontinuity is described in 
http://www.charmm.org/documentation/c39b1/parmfile.html

-Justin

-- 
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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
http://mackerell.umaryland.edu/~jalemkul

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