hi all yes the gro file does have all ions, NA + number of ions equal to CL number. so when i use grep command , i have same number of NA and CL and that what tells me that something is wrong , because i should have another 50 ions of NA extra to neutralize the system
Thank you On Tue, Jul 26, 2011 at 5:03 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Warren Gallin wrote: > >> You are not specifying the ions to be added using the -pname and -nname >> options with the genion command. >> >> Perhaps that is a problem? >> >> > They are not necessary; the default names are used and should be correct > for all force fields now that naming has been standardized. > > Thus far I have seen no evidence that genion is not doing what it is > supposed to. It reports finding a net -50 charge on the system. What > happens then? Does the output coordinate file contain ions? The topology > will not be modified because genion is not being told to (i.e. through the > use of -p). > > -Justin > > > 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://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. 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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? 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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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