[gmx-users] CA ions

[Tasneem Kausar]

You are going to the right way. There are more options given in gmx genion.
Check -pname and -nname. These options will help you to select the name of
positive and negative ions.


On Sat, 7 Dec 2019, 5:05 am Iman Katouzian, <imaneternity at gmail.com> wrote:

> Good day,
>
> I want to simulate my protein in gromacs and in this simulation I need to
> add a certain concentration of CA ions to my system. However, I have no
> idea about how to do this so first I have to neutralize my system and then
> need to add the needed CA ions which act as binding agents* (necessary
> factor in experiments) *in my protein. I have heard that with -neutral and
> -conc for adding the certain concentration I can do this thing.
> I would appreciate it if somebody can help me with this issue.
>
> Thanks.
> --
>
> *Iman Katouzian*
>
> *Ph.D.** candidate of Food Process Engineering*
>
> *Faculty of Food Science and Technology*
>
> *University of Agricultural Sciences and Natural Resources, Gorgan, Iran*
> --
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