[gmx-users] amber to gromacs conversion of LJ potential

[Justin Lemkul]

On 5/14/14, 8:21 PM, Chetan Mahajan wrote:
> Dear All,
>
> While converting LJ parameters from Amber to Gromacs, acpype tool (that is
> used for converting Amber input files into those for gromacs) uses
> following form:
>
> sigma = 2 * r * 2^(-1/6)
>
> I understand the factor 2^(-1/6), but there is another "2" that appears in
> the beginning. Where is that factor coming from? That factor does not arise
> when we choose following forms for LJ potential functions in Amber as well
> as Gromacs.
>

IIRC, Amber stores values in its parameter files as Rmin/2, hence the need to 
multiply by 2.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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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