[gmx-users] Dihedral convention

[Mark Abraham]

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
> >>>
> >>> * Please search the archive at
> >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >>> posting!
> >>>
> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>>
> >>> * For (un)subscribe requests visit
> >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >>> send a mail to gmx-users-request at gromacs.org.
> >>>
> >>>
> > --
> > ==================================================
> >
> > 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
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>