You are not specifying the ions to be added using the -pname and -nname options with the genion command.
Perhaps that is a problem? Warren Gallin On 2011-07-26, at 2:49 PM, Sara baretller wrote: > thanks but i want to neutralize the system , why genion -s file.tpr -conc 0.2 > -neutral -o file.gro -random does not neutralize the system to 0 . > > > On Tue, Jul 26, 2011 at 3:48 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Sara baretller wrote: > Hi > > this a part of the md.log where the system has -50 charge > > two-body bonded interactions: 0.407 nm, Bond, atoms 514 515 > multi-body bonded interactions: 0.731 nm, G96Angle, atoms 1272 1275 > Minimum cell size due to bonded interactions: 0.804 nm > Maximum distance for 9 constraints, at 120 deg. angles, all-trans: 0.810 nm > Estimated maximum distance required for P-LINCS: 0.810 nm > This distance will limit the DD cell size, you can override this with -rcon > Optimizing the DD grid for 4 cells with a minimum initial size of 0.810 nm > The maximum allowed number of cells is: X 11 Y 11 Z 11 > Domain decomposition grid 4 x 1 x 1, separate PME nodes 0 > Domain decomposition nodeid 0, coordinates 0 0 0 > > Table routines are used for coulomb: TRUE > Table routines are used for vdw: TRUE > Using shifted Lennard-Jones, switch between 0.9 and 1.2 nm > Cut-off's: NS: 1.2 Coulomb: 1.2 LJ: 1.2 > System total charge: -50.000 > Generated table with 1100 data points for Shift. > Tabscale = 500 points/nm > Generated table with 1100 data points for LJ6Shift. > Tabscale = 500 points/nm > Generated table with 1100 data points for LJ12Shift. > Tabscale = 500 points/nm > Configuring nonbonded kernels... > Configuring standard C nonbonded kernels... > Testing ia32 SSE2 support... present > > > There's nothing abnormal here. genion reports that it finds a -50 charge on > the system. That's what it's supposed to do. Based on what it finds in the > topology, it adds neutralizing ions and any additional ions to reach the > specified concentration. You only have a problem if grompp later complains > that there's still some residual charge (excluding tiny rounding > discrepancies). > > -Justin > > On Tue, Jul 26, 2011 at 2:18 PM, Justin A. Lemkul <jalem...@vt.edu > <mailto:jalem...@vt.edu>> wrote: > > > > Sara baretller wrote: > > Hi All > > I used the genion command using like this "genion -s file.tpr > -conc 0.2 -neutral -o file.gro -random " again and i checked > the md.log file and it says that the net charge is negative like > it was before using the genion command. > > so can anybody tell me what is wrong with the line genion -s > file.tpr -conc 0.2 -neutral -o file.gro -random . > > > Please copy and paste the exact (pertinent) output from the log file. > > -Justin > > Sara > > > > > On Tue, Jul 26, 2011 at 1:05 PM, Justin A. Lemkul > <jalem...@vt.edu <mailto:jalem...@vt.edu> > <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote: > > > > Sara baretller wrote: > > Hi all > > I used the genion to add a concentration and to neutalize the > system in the same time by using the > > *genion -s file.tpr -conc 0.2 -neutral -o file.gro > -random > so it did add the NA and Cl but it did not > neutralize the > system, the net charge of the system still the same negative. > > > I find this hard to believe. The application of genion -conc > -neutral has worked in every instance I've tried it along every > Gromacs version. Check your output again. > > > so i tried to use the genion seperate to neutralize the > charge using the file.tpr and out file as the file.gro, > however it reset the file.gro and i lose the NA And > CL ions > added for the concentration. > > > Without the actual sequence of commands, this is not a useful > description. genion adds ions based on whatever it finds in > the .tpr > file (which is presumably not neutralized). If you do not > re-create > a .tpr file in between different additions of ions, you're > going to > be undoing work you thought you did. > > -Justin > > -- ==============================____========== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540) > > 231-9080 <tel:%28540%29%20231-9080> > <tel:%28540%29%20231-9080> > > http://www.bevanlab.biochem.____vt.edu/Pages/Personal/justin > <http://vt.edu/Pages/Personal/justin> > > <http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin > <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>> > > ==============================____========== > -- gmx-users mailing list gmx-users@gromacs.org > <mailto:gmx-users@gromacs.org> > <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>> > > > http://lists.gromacs.org/____mailman/listinfo/gmx-users > <http://lists.gromacs.org/__mailman/listinfo/gmx-users> > <http://lists.gromacs.org/__mailman/listinfo/gmx-users > <http://lists.gromacs.org/mailman/listinfo/gmx-users>> > Please search the archive at > http://www.gromacs.org/____Support/Mailing_Lists/Search > <http://www.gromacs.org/__Support/Mailing_Lists/Search> > <http://www.gromacs.org/__Support/Mailing_Lists/Search > <http://www.gromacs.org/Support/Mailing_Lists/Search>> before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org > <mailto:gmx-users-requ...@gromacs.org> > <mailto:gmx-users-request@__gromacs.org > <mailto:gmx-users-requ...@gromacs.org>>. > > Can't post? Read > http://www.gromacs.org/____Support/Mailing_Lists > <http://www.gromacs.org/__Support/Mailing_Lists> > <http://www.gromacs.org/__Support/Mailing_Lists > <http://www.gromacs.org/Support/Mailing_Lists>> > > > > -- ==============================__========== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 > <tel:%28540%29%20231-9080> > http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin > <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================__========== > -- gmx-users mailing list gmx-users@gromacs.org > <mailto:gmx-users@gromacs.org> > http://lists.gromacs.org/__mailman/listinfo/gmx-users > <http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at > http://www.gromacs.org/__Support/Mailing_Lists/Search > <http://www.gromacs.org/Support/Mailing_Lists/Search> before posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org > <mailto:gmx-users-requ...@gromacs.org>. > Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists > <http://www.gromacs.org/Support/Mailing_Lists> > > > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? 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