I use these two lines to neutralise the system
$ gmx grompp -f minimization.mdp -r system-solvated.gro -c system-solvated.gro -p system.top -o system_genion.tpr $ echo W | gmx genion -s system_genion.tpr -o system_genion.gro -p system.top -pname NA -nname CL -neutral -conc 0.2 (#include "martini_v2.0_ions.itp") is shown in the system.top file. However, I found out that the above two lines could still work after removing the (#include "martini_v2.0_ions.itp"). Also, I can change "NA" and "CL" to any other names without any errors. So how the CG ions are reflected in the CG system? I think the CG ions are different from the all-atom ions, right? -- 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.
