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, <imanetern...@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* > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
