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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