Copy the output from both of those commands, most importantly (as Mark has asked) that from the first one gmx grompp
You need to show people exactly what you are seeing, not what you say you are seeing. The latter you are filtering it, and most likely not providing all the important information. The former allows those trying to help to see all the information that they need to see. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. On 2 August 2017 at 04:05, Ali Ahmed <aa5635...@gmail.com> wrote: > Hi, > Thank you for your help. > > well I used this command > > gmx grompp -f em.mdp -c box.gro -p topol.top -o em.tpr > gmx mdrun -v -deffnm em > > and I got all the warnings. Here is my em.mdp > ------------------------------------------------------------------------------------- > > integrator = steep > > emtol = 10.0 > > emstep = 0.001 > > nsteps = 50000 > > energygrps = system > > ; Parameters describing how to find the neighbors of each atom and how to > calculate the interactions > > nstlist = 1 > > cutoff-scheme = group > > ns_type = grid > > coulombtype = PME > > rcoulomb = 1.0 > > rvdw = 1.0 > > pbc = xyz > > On Tue, Aug 1, 2017 at 11:07 AM, Mark Abraham <mark.j.abra...@gmail.com> > wrote: > >> Hi, >> >> No, only mdrun issues LINCS warnings. grompp issues different warnings, and >> I would like you to check whether you had any from grompp that you may not >> have considered. :-) >> >> Mark >> >> On Tue, Aug 1, 2017 at 5:04 PM Ali Ahmed <aa5635...@gmail.com> wrote: >> >> > 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. >> > >> -- >> 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.
