Dear Justin I have tried same what you have said. I followed the tutorial for CO2 but didn't work, gave an error during the energy minimization . I'm not sure what was the wrong, I noticed the N atoms (in the box) were separated from the virtual site after the error.
On Mon, Jul 17, 2017 at 10:41 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/17/17 11:38 AM, Ali Ahmed wrote: > >> Dear Justin >> Thank you very much. As I saw in some literature (as in the link below) >> that N atom has a negative charge and needs a massless positive charge. I >> tried with most of the FFs but could not produce nitrogen density above >> critical point. I don'n know which FF is the best one and I'm new to MD >> simulations and new GROMACS user. >> Could you please tell me which FF should I use? >> > > What you're citing is a custom model. You can write the force field files > very easily. I see what you're trying to do now, but you should be clear > that N2 is not a negatively charged molecule simply because the N atoms (in > this representation) have partial negative charges. The virtual site > balances it out so that electrostatic properties are better represented. > > The virtual site you need to create is a simple one, placed at the center > of the N-N bond, so this is virtual_sites2 with an "a" value of 0.5. > > -Justin > > > Thank you very much I appreciate your support. >> >> http://iopscience.iop.org/article/10.1088/0965-0393/24/4/045002/meta >> >> On Mon, Jul 17, 2017 at 8:40 AM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> 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. >>> >>> > -- > ================================================== > > 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. > -- 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.