[gmx-users] Re: I need help for gromacs

Justin A. Lemkul jalemkul at vt.edu
Sat Aug 8 16:53:03 CEST 2009

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 

Veli Celik wrote:
> Hello,
> 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:
> ı
> 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;
> genion -s EM.tpr -o oution.gro -pname NA+
> but i get the error
> "No ions to add and no potential to calculate."

You haven't told genion what to do.  Use the -np flag to specify how many ions 
you want placed into your system.

> 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?

There are numerous tutorials available online.  I suggest you run through a few 
of them:


You may also find some useful information about CNTs here:



> I will be very happy if you can help.
> thx.


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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