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

Lili Peng lpeng at ucsd.edu
Sat Aug 8 19:58:17 CEST 2009

Hi Veli,

Try this:

genion -s EM.tpr -o oution.gro -np <your number of ions> -random

Select "3" to replace the water molecules with ions.
(Make sure you update your number of water molecules and ions in your
topol.top file.)

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 :).

Good luck,

2009/8/8 Justin A. Lemkul <jalemkul at vt.edu>

> 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.
> 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:
> http://oldwiki.gromacs.org/index.php/Category:Tutorials
> You may also find some useful information about CNTs here:
> http://oldwiki.gromacs.org/index.php/Carbon_Nanotube
> -Justin
>  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
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
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