Hello,<br><br>Greetings from Pawan.<br>-np is a parameter used to add the nmber of positive ions.<br>when u have -4 negative charge u should give -np 4.<br>-np with -pname will be more appropriate.<br>see through this website for the proper usage of genion options.<br>
<a href="http://www.gromacs.org/documentation/reference_3.3/online/genion.html">http://www.gromacs.org/documentation/reference_3.3/online/genion.html</a><br><br>Regards,<br>Pawan<br><div class="gmail_quote">On Fri, May 22, 2009 at 3:20 PM, Stefano Meliga <span dir="ltr"><<a href="mailto:smeliga@gmail.com">smeliga@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Dear all,<br>
<br>
As the on-screen output of grompp says, my system has non-zero total charge = -4.000<br>
<br>
Thus, I'm trying to neutralize the system using genion with this command line:<br>
<br>
genion -s 4AKEallHsol.tpr -o 4AKEallHion.gro -p 4AKEallHsol_pre.top -neutral<br>
<br>
The problem is that the on-screen output says:<br>
<br>
"No ions to add and no potential to calculate"<br>
as the system was already neutral, I guess.<br>
<br>
I then tryied with the command line:<br>
<br>
genion -s 4AKEallHsol.tpr -o 4AKEallHion.gro -p 4AKEallHsol_pre.top -neutral -np 50 -g<br>
<br>
Ions are added to the SOL group but the total charge remains -4, as the log file says.<br>
<br>
Do you know the reason?<br>
<br>
Thanks a lot,<br>
<br>
Stefano<br>
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</blockquote></div><br>