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 <jalem...@vt.edu
<mailto:jalem...@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>
==============================__==========
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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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