[gmx-users] (no subject)

[Justin A. Lemkul]

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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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

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