[gmx-users] (no subject)

[Sara baretller]

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

On Tue, Jul 26, 2011 at 2:18 PM, Justin A. Lemkul <jalemkul at 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 <jalemkul at vt.edu<mailto:
>> jalemkul at 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> | (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>
>> >
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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
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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