[gmx-users] hydrocarbons simulation

[Justin Lemkul]

On 4/11/15 3:34 AM, saly jackson wrote:
> Dear all
>
> Hope you are fine.
>
> To define an alkane molecule such as hexane I have defined its bonds,
> angles and cdihedrales according to amber forcefield. for non-bonded
> interactions I also have defined LJ and Columbic pair potentials.
> I am wondering if we need to consider special bonds for alkanes such as
> n-hexane and n-decane?
>

What exactly would constitute a "special bond" in an alkane?

-Justin

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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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