[gmx-users] (no subject)

[Justin A. Lemkul]

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.

-Justin

> Sara
> 
> 
> 
> 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
> 
>     -- 
>     ==============================__==========
> 
>     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
>     <tel:%28540%29%20231-9080>
>     http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>     <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> 
>     ==============================__==========
>     -- 
>     gmx-users mailing list    gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://lists.gromacs.org/__mailman/listinfo/gmx-users
>     <http://lists.gromacs.org/mailman/listinfo/gmx-users>
>     Please search the archive at
>     http://www.gromacs.org/__Support/Mailing_Lists/Search
>     <http://www.gromacs.org/Support/Mailing_Lists/Search> before posting!
>     Please don't post (un)subscribe requests to the list. Use the www
>     interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
>     <http://www.gromacs.org/Support/Mailing_Lists>
> 
> 

-- 
========================================

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

========================================