[gmx-users] (no subject)
Justin A. Lemkul
jalemkul at vt.edu
Tue Jul 26 20:18:12 CEST 2011
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.
> On Tue, Jul 26, 2011 at 1:05 PM, Justin A. Lemkul <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 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
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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