Hello,<br><br>Greetings from Pawan.<br>Giving the command and the options being used will be much better to give any further probable suggestions. <br>Just using " -np 4 " wont solve the problem as such. You should specify the " -pname " option also. You can use NA+ ions to neutralize the system as its having negative charge. And when specifying the -np or -nn option u need not use -neural option.<br>
<br>Regards,<br>Pawan<br><br><br><br><div class="gmail_quote">On Fri, May 22, 2009 at 4:30 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;">
Thanks Pawan,<br>
<br>
I added 4 positive ions as you suggested but the system total charge reported in genion.log is still -4!<br>
<br>
Why?<br>
<br>
Cheers,<br>
<br>
Stefano<br>
<br>
<br>
Pawan Kumar ha scritto:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">
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" target="_blank">http://www.gromacs.org/documentation/reference_3.3/online/genion.html</a><br>
<br>
Regards,<br>
Pawan<br></div><div class="im">
On Fri, May 22, 2009 at 3:20 PM, Stefano Meliga <<a href="mailto:smeliga@gmail.com" target="_blank">smeliga@gmail.com</a> <mailto:<a href="mailto:smeliga@gmail.com" target="_blank">smeliga@gmail.com</a>>> wrote:<br>
<br>
Dear all,<br>
<br>
As the on-screen output of grompp says, my system has non-zero<br>
total charge = -4.000<br>
<br>
Thus, I'm trying to neutralize the system using genion with this<br>
command line:<br>
<br>
genion -s 4AKEallHsol.tpr -o 4AKEallHion.gro -p<br>
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<br>
4AKEallHsol_pre.top -neutral -np 50 -g<br>
<br>
Ions are added to the SOL group but the total charge remains -4,<br>
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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