Thank you Parham You mean that it is not necessary to do QM/MM simulation?
On Tuesday, March 8, 2016 11:13 AM, Parham Jabbarzadeh (Department of Biomedical Science) <pjabbarza...@gmail.com> wrote: Dear Sir Use this command: gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -neutral In this case, you don't need the number of ions. Kind Regards Parham J. K. ========================= PhD candidate - Lecturer in drug discovery Faculty of Medicine and Health SciencesUniversity Putra MalaysiaMalaysia =========================Publication ::: Featured Publication ::: Website ::: FaceBook On Tue, Mar 8, 2016 at 3:32 PM, mohammad r <mohammad.r0...@yahoo.com> wrote: Hi everybody, I’ve generated a water-peptide system, now I want to neutralize it. Is adding adequate number of ions sufficient for neutralizing process or I should do QM/MM simulation for the this process? Thank you, Mohammad. -- 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.