Dear Sako, it has been parameterized already: http://scitation.aip.org/content/aip/journal/jcp/141/24/10.1063/1.4904545
obviously, you need to check if their parameters work for QDs (they have tested them for periodic solids). You should check if the resulting QD still has some degree of crystalline order inside, larger distortions at the surface are acceptable. best Andre On Sun, Oct 16, 2016 at 8:00 PM, SAKO MIRZAIE <sako.bioc...@gmail.com> wrote: > 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 <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 > >> 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 > > > > jalem...@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/ > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- _____________ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
