[gmx-users] Dihedral convention

[Christopher Neale]

Where? I took a look at v5.1.2 manual section 4.2.12 and could not find it, hence my suggestion to test it out. I note that there is indeed some definition in section 4.2.13: "Proper dihedral angles are defined according to the IUPAC/IUB convention, where φ is the angle
between the ijk and the jkl planes, with zero corresponding to the cis configuration (i and l onthe same side)." -- but that specifies that it relates to propers and also it doesn't exactly answer the OP's question about ranges from 0-360 or -180 to +180. Everything is also complicated by the RB definition "where ψ = φ − 180◦", so now it is clear that an "angle" does not always have the same definition.

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Mark Abraham <mark.j.abraham at gmail.com>
Sent: 14 April 2016 14:44
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Dihedral convention

Hi,

Also, the details of angle conventions are all covered in the reference
manual.

Mark

On Thu, 14 Apr 2016 20:37 Christopher Neale <chris.neale at alum.utoronto.ca>
wrote:

> Make a box with a single molecule of n-butane, no pressure coupling or
> pme, use the sd integrator, test it out?
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Parvez Mh
> <parvezmh89 at gmail.com>
> Sent: 14 April 2016 12:47
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Dihedral convention
>
> Dr. Lemkul,
>
> I understand what you said. My question is, in function type 2 ,there are
> two parameters 1) force constant and 2) angle of plane. For angle
> measurement, which convention does gromacs follow, -180 t0 180 or 0 to 360?
>
> --Masrul
>
> On Wed, Apr 13, 2016 at 8:35 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 4/13/16 8:29 PM, Parvez Mh wrote:
> >
> >> I am talking about improper dihedral function type 2.
> >>
> >>
> > Impropers are intended to keep planar groups planar, not to restrict
> other
> > geometries.  You would be better off with a normal dihedral restraint or
> > potentially figuring out why your force field isn't preserving the
> desired
> > geometry.
> >
> > -Justin
> >
> >
> > --Masrul
> >>
> >> On Wed, Apr 13, 2016 at 7:21 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >>
> >>
> >>>
> >>> On 4/13/16 2:51 PM, Parvez Mh wrote:
> >>>
> >>> Dear all:
> >>>>
> >>>> I would like to  use a harmonic type potential for dihedral. Should i
> >>>> use
> >>>> angle value (-180 to 180 ) or (0 to 360) convention. My equilibrium
> >>>> angle
> >>>> is -64 degree. then what would be the angle -64 or (-64+360=)296
> degree?
> >>>>
> >>>>
> >>>> Unless you're writing your own code for new functions, there is no
> such
> >>> thing as a harmonic dihedral.  See the manual, Chapter 4, for available
> >>> functional forms.
> >>>
> >>> -Justin
> >>>
> >>> --
> >>> ==================================================
> >>>
> >>> 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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> >>>
> > --
> > ==================================================
> >
> > 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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