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

[SAKO MIRZAIE]

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.

best regards,

On Mon, Oct 17, 2016 at 1:22 AM, Justin Lemkul <jalemkul at 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
>> 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
>
> --
> ==================================================
>
> 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
>
> ==================================================
>



-- 
***********************************************
Sako Mirzaie
PhD in biochemistry, Assistant Professor, science faculty, Islamic Azad
university of
Sanandaj, Sanandaj, Iran

http://www.iausdj.ac.ir/fa/fa-info.aspx?p=s.mirzaie

http://www.iausdj.ac.ir/en/en.aspx?p=s.mirzaie

http://scholar.google.com/citations?user=viwZvVAAAAAJ&hl=en

http://www.scopus.com/authid/detail.url?authorId=54886431500

http://www.ncbi.nlm.nih.gov/pubmed/?term=sako+mirzaie
https://www.researchgate.net/profile/Sako_Mirzaie/publications/