[gmx-users] Dihedral convention

Mon Apr 18 12:59:37 CEST 2016

Hi,
On Thu, 14 Apr 2016 21:10 Christopher Neale <chris.neale at alum.utoronto.ca>
wrote:

> 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

Impropers are defined in the previous section, which refers to the one you
quote, where phi is defined clearly.

> and also it doesn't exactly answer the OP's question about ranges from
> 0-360 or -180 to +180.

This doesn't matter at all. cos(n * phi + phi_0) is invariant under any
increment to phi or phi_0 by an increment of a multiple of a full rotation,
because n is an integer.

> 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.
>

That's life. RB has its roots in the polymer simulation community, who use
a different convention from biomolecular folks. I'm open to ways to improve
the wording, though.

Mark

> ________________________________________
> 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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