Hi Veli,<br><br>Try this:<br><br>genion -s EM.tpr -o oution.gro -np <your number of ions> -random<br><br>Select "3" to replace the water molecules with ions.<br>(Make sure you update your number of water molecules and ions in your topol.top file.)<br>
<br>When you're learning Gromacs it's probably a good idea to consult tutorials online first. If the tutorials still don't address your problem, don't be shy about addressing gmx-users because other people on this discussion list probably have had or will have the same problem as you :).<br>
<br>Good luck,<br>-L<br><br><div class="gmail_quote">2009/8/8 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
Please keep all Gromacs-related correspondence on the gmx-users list. As I said not two days ago (and dozens of times before), I do not advertise myself as an all-knowing private tutor. You are much better served posting questions to the list.<br>
<br>
Veli Celik wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hello,<br>
<br>
I am a student and trying to learn how to use gromacs for my project. I got stuck at one point and don't have anyone to ask around me. Therefore I searched the internet and saw that you also had a similar problem before. Therefore, I will be very happy if you can guide me. Here is my problem:<br>
ı<br>
I am trying to put ions into a carbon nano tube. I have generated the tube, put water in it first and did the energy minimization using grompp. So I have a tpr file. Now I need to use the genion command to replace the water molecules with ions. What is the proper way of doing that? I have tried the following command;<br>
<br>
genion -s EM.tpr -o oution.gro -pname NA+<br>
<br>
but i get the error<br>
<br>
"No ions to add and no potential to calculate."<br>
<br>
</blockquote>
<br>
You haven't told genion what to do. Use the -np flag to specify how many ions you want placed into your system.<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
I am new to gromacs and not used genion before. What should I do? Do nee to include the ions in a file or specify a potential? If so how?<br>
<br>
</blockquote>
<br>
There are numerous tutorials available online. I suggest you run through a few of them:<br>
<br>
<a href="http://oldwiki.gromacs.org/index.php/Category:Tutorials" target="_blank">http://oldwiki.gromacs.org/index.php/Category:Tutorials</a><br>
<br>
You may also find some useful information about CNTs here:<br>
<br>
<a href="http://oldwiki.gromacs.org/index.php/Carbon_Nanotube" target="_blank">http://oldwiki.gromacs.org/index.php/Carbon_Nanotube</a><br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
I will be very happy if you can help.<br>
<br>
thx.<br>
<br>
<br>
</blockquote>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
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</blockquote></div><br>