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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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