[gmx-users] Non-bonded interactions

[Justin Lemkul]

On 12/20/14 9:12 AM, Doa Hawamdeh wrote:
> Dear All,
>   I want to use GROMACS 5.0.3 to simulate charged groups in my system, what
> are the types of the nonbonded interactions (lennard-Jones and coulomb)
> that I have to use??
>

All biomolecular force fields in Gromacs were parametrized to include LJ and 
Coulombic interactions in their functional forms, so I don't really know what 
can be the question here.  The methods for calculating those forces/energies 
vary between force fields, but those algorithms and cutoff lengths are fixed 
aspects of the force field that you use based on what the force field literature 
tells you.

-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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