Dear Justin I have checked and tried but still not working, it says ( invalid order for directive atomtypes). Please can you take a look on the following -------------------------------------------------------- Here is the topology file
;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 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 M M 0.000 0.000 V 0.000 0.000 ; [ 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 M 1 N_2 M1 1 0.482 0.0000 ; MN is the virtual site 4 M 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 1 2 1 0.11 [ system ] Nitrogen in vacuo [ molecules ] N_2 1000 ----------------------------------------------------------------------------------------------------- here is the pdb file TITLE N_2 with dummy masses REMARK THIS IS A SIMULATION BOX CRYST1 50.000 50.000 50.000 90.00 90.00 90.00 P 1 1 MODEL 1 ATOM 1 N1 N_2 1 0.000 0.000 0.000 1.00 0.00 ATOM 2 N2 N_2 1 1.100 0.000 0.000 1.00 0.00 ATOM 3 M1 N_2 1 0.200 0.000 0.000 1.00 0.00 ATOM 4 M2 N_2 1 0.900 0.000 0.000 1.00 0.00 TER ENDMDL ----------- Thank you On Tue, Jul 18, 2017 at 8:10 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/17/17 3:39 PM, Ali Ahmed wrote: > >> 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 >> >> > This is incorrect; the virtual site should be particle type V, not A. > > >> >> [ 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 >> >> > This is why your system is failing. You're defining a constraint between > the virtual sites and no bonded interaction at all between the N atoms. If > the N-N bond is to be constant at 0.11 nm, then set it as a constraint > (between atoms 1 and 2) and construct the virtual sites based on the real > atoms in the system. > > -Justin > > > [ 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. >>> >>> > -- > ================================================== > > 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? 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