[gmx-users] Dihedral convention
jalemkul at vt.edu
Thu Apr 14 03:36:02 CEST 2016
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.
> 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 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
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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
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