Dear Mark Yes, all the warnings are from grompp. I have no idea where is the problem in the structure or the topology Thank you
On Mon, Jul 31, 2017 at 2:34 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > Did you get any warnings from grompp? > > Mark > > On Mon, Jul 31, 2017 at 5:48 PM Ali Ahmed <aa5635...@gmail.com> wrote: > > > Hello GROMACS users, > > > > I'm doing MD for nitrogen, and for better electrostatic interactions I > need > > to use massless and charged virtual site. I did that but when I try to do > > energy minimization gives me LINCS warning and crush. I don't know where > is > > the error I tried a lot but could not find a solution. > > Anyone has an idea where is my error > > > > Here is the topology file (hand written) > > > > ------------------ > > > > [ defaults ] > > > > 1 3 yes 0.5 0.5 > > > > ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; > ;;;;;;;;;;;;; > > > > [ atomtypes ] > > > > ; name bond_type mass charge ptype sigma epsilon > > > > OP OP 0.000 0.000 A 0.330 0.3062 ; > > nitrogen > > > > M M 0.000 0.000 V 0.000 0.000 > ; > > virtual site > > > > > > ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; > ;;;;;;;;;;;;;;;; > > > > [ moleculetype ] > > > > ; name nrexcl > > > > N2 2 > > > > > > > > [ atoms ] > > > > ; nr type resnr residue atom cgnr charge mass > > > > 1 OP 1 N2 N1 1 -0.482 14.0067 > > > > 2 M 1 N2 M1 1 0.964 0.000 > > > > 3 OP 1 N2 N2 1 -0.482 14.0067 > > > > > > > > [ constraints ] > > > > ; the N-N is fixed > > > > 1 3 1 0.11 > > > > > > > > [ virtual_sites2 ] > > > > ; site ai aj funct a > > > > 2 1 3 1 0.5000 ; right in the mid > > > > > > > > ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; > > > > [ system ] > > > > N2 in vacuo > > > > > > > > [ molecules ] > > > > N2 1500 > > > > ------------------------------------------------------------ > > -------------------------------------- > > > > Here is the structure (N2.pdb) > > > > ----------- > > > > TITLE N2 with dummy masses > > > > REMARK THIS IS A SIMULATION BOX > > > > MODEL 1 > > > > COMPND UNNAMED > > > > AUTHOR GENERATED BY OPEN BABEL 2.3.2 > > > > CRYST1 50.000 50.000 50.000 90.00 90.00 90.00 P 1 1 > > > > ATOM 1 N1 N2 1 0.000 0.000 0.000 1.00 > > 0.00 N > > > > ATOM 2 M1 N2 1 0.55000 0.000 0.000 1.00 > > 0.00 Xx > > > > ATOM 3 N2 N2 1 1.100 0.000 0.000 1.00 > > 0.00 N > > > > CONECT 1 3 > > > > CONECT 3 1 > > > > MASTER 0 0 0 0 0 0 0 0 3 0 3 0 > > > > END0 > > > > ------------------------------------------------------------ > > --------------------------------- > > Thank you > > -- > > 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.