Re: [gmx-users] Silica Nanoparticles
On 4/22/14, 11:12 AM, Kazem Sepehrinia wrote: Hi Dear All, Have any of you guys prepared silica nanoparticles in your Molecular Simulation studies? I used some open databases for obtaining of bulk amorphous silica file. But i'm not able to prepare silica nanoparticles. Once again i used materials studio glasses and made a nanoparticle but that one is not working also. Because i tried to minimize it and job failed. Any help would be greatly appreciated. You'll have to define not working and job failed in more detail. Is something crashing? Are there problems with topology generation? Using pdb2gmx to create a topology will likely be a major pain, since it is designed for (mostly) linear polymers, though g_x2top might handle it alright, provided you have written a suitable .n2t file. These are all the sorts of things we need to know to provide useful advice. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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.
Re: [gmx-users] Silica Nanoparticles
You may try to use special potential designed for amorphous silica: A numerical investigation of the liquid–vapor coexistence curve of silica Yves Guissani and Bertrand Guillot J. Chem. Phys. 104, 7633 (1996) On 22 April 2014 17:12, Kazem Sepehrinia ksepehri...@gmail.com wrote: Hi Dear All, Have any of you guys prepared silica nanoparticles in your Molecular Simulation studies? I used some open databases for obtaining of bulk amorphous silica file. But i'm not able to prepare silica nanoparticles. Once again i used materials studio glasses and made a nanoparticle but that one is not working also. Because i tried to minimize it and job failed. Any help would be greatly appreciated. Thanks, Kazem Sepehrinia. -- 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. -- 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.
Re: [gmx-users] Silica Nanoparticles
Dear Mehmet, Thank you for replying. -Kazem On Tue, Apr 22, 2014 at 2:07 PM, Suzen, Mehmet msu...@gmail.com wrote: You may try to use special potential designed for amorphous silica: A numerical investigation of the liquid–vapor coexistence curve of silica Yves Guissani and Bertrand Guillot J. Chem. Phys. 104, 7633 (1996) On 22 April 2014 17:12, Kazem Sepehrinia ksepehri...@gmail.com wrote: Hi Dear All, Have any of you guys prepared silica nanoparticles in your Molecular Simulation studies? I used some open databases for obtaining of bulk amorphous silica file. But i'm not able to prepare silica nanoparticles. Once again i used materials studio glasses and made a nanoparticle but that one is not working also. Because i tried to minimize it and job failed. Any help would be greatly appreciated. Thanks, Kazem Sepehrinia. -- 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. -- 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. -- 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.
