[gmx-users] (no subject)
Sara baretller
sarabiocomputation at gmail.com
Tue Jul 26 22:49:01 CEST 2011
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 <jalemkul at 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 <jalemkul at vt.edu<mailto:
>> 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>
>> <mailto: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> <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>
>> >>
>>
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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 <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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