On 7/16/17 9:20 PM, Ali Ahmed wrote:
Hello GROMACS users, This is Ali, I'm new to Gromacs and doing MD simulation of nitrogen at super critical point.The structure I use is different from regular nitrogen (N-N). As you know N atom has a negative charge which means the nitrogen molecule will be negatively charged, therefore I need to use massless and
This is incorrect - N2 carries no formal charge.
charged virtual site to equilibrate the molecule. I have looked on the tutorial about CO2 to produce the XXX.itp but didnot work with me. Could anyone have done it before tell me how to do it ?
You don't need virtual sites for a diatomic molecule. -Justin
Here are the parameters: N :mass =14.0067, epsilon =(0.3026 KJ/mol), sigma =(0.332 nm), Charge =(-0.482 e). XX (massless, charged particle ):mass =0, epsilon=0, sigma=0 Charge= 0.964 e. Thank you very much.
-- ================================================== 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 ================================================== -- 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.
