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.