[gmx-users] Re: I need help for gromacs
Justin A. Lemkul
jalemkul at vt.edu
Sat Aug 8 20:03:24 CEST 2009
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:
Lots of useful information there.
> Good luck,
> 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:
> 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:
> 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
> 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.
> 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
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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