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://vt.edu/Pages/Personal/justin> >> > >> >> <http://www.bevanlab.biochem._**_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> >> > >> >> <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> >> > >> >> <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-request@**gromacs.org<gmx-users-requ...@gromacs.org> >> > >> <mailto:gmx-users-request@__gr**omacs.org <http://gromacs.org> >> <mailto:gmx-users-request@**gromacs.org<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> >> > >> >> <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://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> >> >> 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-request@**gromacs.org<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 | (540) 231-9080 > 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 > 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. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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