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 <[email protected] <mailto:[email protected]>>
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
========================================
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