[gmx-users] parameters for PbSe (quantum dot)

[Justin Lemkul]

On 10/15/16 1:35 PM, SAKO MIRZAIE wrote:
> Dear all,
>
> I want to simulate the quantum dot PbSe (QD) by gromacs and amber 99sb FF.
> but, as you know, gromacs doesn't know this QD and its MD parameters is not
> exist. how can I find the Lennard jones parameters and partial charges for
> this QD?
>

I don't think there's anything in AMBER99sb (or any biomolecular force field, 
for that matter) that will be of use to you.  For something like PbSe, if 
parameters don't already exist in the materials community, you have to 
parametrize them completely de novo.  You'll need some form(s) of target data - 
structural, energetic, etc. to be able to know if you're on the right track.

-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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