Dear Justin Here is the topology file I wrote. I included all the parameters rather than use a specific FF.
Thank you for your support .. ------------------------------------------------------------------------------------------------------------------------- ; virtual sites have zero mass which leads to zero Moment of inertia ;virual sites have charge only 0.482 e. to balance the nitrogen atom negative charge -0.482 e. ; the distance between two nitrogn atoms N--N is 0.11 nm ;the distance between two virtual sites is 0.15 nm ;the distance between nitrogen atom and virtual site is 0.02 nm. This makes the virtual site attached to the nitrogen atom ; [ atomtypes ] ; name bond_type mass charge ptype sigma epsilon N N 0.000 0.000 A 0.332 0.3026 MN MN 0.000 0.000 A 0.000 0.000 ; MN is the virtual sites [ moleculetype ] ; name nrexcl N_2 2 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 N 1 N_2 N1 1 -0.482 14.0067 2 N 1 N_2 N2 1 -0.482 14.0067 3 MN 1 N_2 M1 1 0.482 0.0000 4 MN 1 N_2 M2 1 0.482 0.0000 [ constraints ] ; There are no bonds in this system ; Instead, we fix the distance between the mass centers such that ; the virtual sites can be reconstructed 3 4 1 0.15 [ system ] CO2 in vacuo [ molecules ] N_2 30 On Mon, Jul 17, 2017 at 12:46 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/17/17 12:31 PM, Ali Ahmed wrote: > >> 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. >> >> > If you have just N2 in a box in vacuo, then this would suggest a topology > problem. Please post the exact text of your .itp file. It should be quite > short and easy to spot any problems. > > -Justin > > > >> 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. >>> >>> > -- > ================================================== > > 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? 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