Thank you. is there any tutorial to do that? I know I should do it with
Quantum mechanics (e.g. gaussian package), but I don't know how.
On Mon, Oct 17, 2016 at 1:22 AM, Justin Lemkul <jalem...@vt.edu> wrote:
> 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
>> 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 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
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
PhD in biochemistry, Assistant Professor, science faculty, Islamic Azad
Sanandaj, Sanandaj, Iran
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