[gmx-users] Dihedral convention

Christopher Neale chris.neale at alum.utoronto.ca
Mon Apr 18 20:25:58 CEST 2016 

Dear Mark:

I don't mean to carry this thread beyond its natural life, but I think the OP is referring to improper dihedrals, harmonic type and not to improper dihedrals, periodic type (or maybe I just don't get how "cos(n * phi + phi_0)" is related to the harmonic type?)

Regarding an improper harmonic type defined in eq. 4.5.9 in section 4.2.12, the manual text only seems like a complete definition if:
(1) there is no such thing as zeta<0 -- this actually makes sense to me, but I think I was thrown off by the x-axis of Fig. 4.9, whose label should probably be "zeta_ijkl - zeta_0" (as opposed to simply reading as "zeta"). Just to clarify, this Fig. 4.9 is referred to in the text above as relating to the improper harmonic type.
(2) it's obvious how to distinguish between zeta=60 and zeta=120 -- this I don't understand. Both angles exist so how do you decide which one to choose?
(3) Whether or not zeta values of 20, -20, 340, and 380 are all considered to represent the same state -- this seems to me like it has a component of programming choice in it, so it might be useful to define that choice, although one that I admit is easy to test.

Thank you,
Chris.
________________________________________
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: 18 April 2016 06:59
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Dihedral convention

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
> > >>>
> > >>> ==================================================
> > >>> --
> > >>> Gromacs Users mailing list
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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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