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

[Justin A. Lemkul]

Lili Peng wrote:
> Hi Veli,
> 
> Try this:
> 
> genion -s EM.tpr -o oution.gro -np <your number of ions> -random
> 

Using -pname and -nname appropriately will override the default ion names, which 
correspond to ffgmx.

> 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.)
> 

Perhaps the group is 3, perhaps it is not.  In any case, replace solvent 
molecules.  Using -p will update the topology automatically.

> 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 :).
> 

Indeed.  As well, the archives can still be searched using the old interface:

http://oldwww.gromacs.org/swish-e/search/search2.php

Lots of useful information there.

-Justin

> Good luck,
> -L
> 
> 2009/8/8 Justin A. Lemkul <jalemkul at vt.edu <mailto: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 <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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> 

-- 
========================================

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

========================================