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

Justin Lemkul jalemkul at vt.edu
Fri Sep 6 23:34:29 CEST 2013

On 9/6/13 2:11 PM, prateekj wrote:
> Hi,
> 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.

In principle, no, but you can convince yourself of this fact with a simple 
single-point energy calculation.

> 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?).

Dihedrals are often not very transferable; proceed with caution.

> 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.

My understanding has always been what is in manual section 4.2.12, in which case 
pairs are used for OPLS-AA, but not for other force fields like GROMOS (but only 
in the case of alkanes).  You can set up a test system with pdb2gmx and a simple 
.rtp entry to see what it generates.  The code should adhere to the force field 



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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