[gmx-users] (no subject)

Justin A. Lemkul jalemkul at vt.edu
Tue Jul 26 19:05:26 CEST 2011

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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