# [gmx-users] Dihedral convention

Christopher Neale chris.neale at alum.utoronto.ca
Thu Apr 14 20:37:11 CEST 2016

```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
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>>> 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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