Hi All<br><br>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.<br>
<br>so can anybody tell me what is wrong with the line genion -s file.tpr -conc 0.2 -neutral -o file.gro -random . <br><br>Sara<br><br><br><br><div class="gmail_quote">On Tue, Jul 26, 2011 at 1:05 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im"><br>
<br>
Sara baretller wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi all<br>
<br>
I used the genion to add a concentration and to neutalize the system in the same time by using the<br>
<br>
*genion -s file.tpr -conc 0.2 -neutral -o file.gro -random <br>
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.<br>
<br>
</blockquote>
<br></div>
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.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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.<br>
<br>
</blockquote>
<br></div>
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.<br>
<br>
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
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