[gmx-users] (no subject)

Sara baretller sarabiocomputation at gmail.com
Tue Jul 26 20:16:58 CEST 2011

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

so can anybody tell me what is wrong with the line  genion -s file.tpr -conc
0.2 -neutral -o file.gro -random .


On Tue, Jul 26, 2011 at 1:05 PM, Justin A. Lemkul <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
> 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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