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
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> 
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>           <tel:%28540%29%20231-9080>
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>    --     ==============================__==========
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>    Justin A. Lemkul
>    Ph.D. Candidate
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>    MILES-IGERT Trainee
>    Department of Biochemistry
>    Virginia Tech
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> -- 
> ========================================
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> 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
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