Sara baretller wrote:
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


I've never seen genion do anything like this. If you send me your .tpr file (off-list) I will see if I can uncover what's going on. I also need to know which Gromacs version you're using.

-Justin

Thank you



On Tue, Jul 26, 2011 at 5:03 PM, Justin A. Lemkul <jalem...@vt.edu <mailto: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 <mailto: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>
            <mailto: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>>
                  <mailto: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

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