[gmx-users] Re: I need help for gromacs
lpeng at ucsd.edu
Sat Aug 8 19:58:17 CEST 2009
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
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 :).
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:
>> 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 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:
> 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 | (540) 231-9080
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