Hi, In general, run "gmx help tool" to see how the tool should be run, here to see that there's an option for you to choose a non-default charge
Mark On Fri, 16 Jun 2017 14:21 Justin Lemkul <jalem...@vt.edu> wrote: > > > On 6/16/17 7:14 AM, Quyen V. Vu wrote: > > Dear GMX developer, > > I don't know this mailing list is suitable for posting issue or not, if > > not- forgive me. > > > > I want to report about gmx genion module > > > > If i want to add concentration of salt by -conc option, it just correct > for > > monovalent salt (eg. NACL). > > > > For multivalent salt(MGCL2), if I use -pname MG -nname CL -conc X > -neutral > > , it wil treat MG as monovanlent cation and give the wrong number of ions > > add into my system, so I have to use -np and -nn option to get correct > the > > number of ions. > > > > If you set the correct value of -pq then you'll get the right result. > genion > defaults to assuming everything is monovalent and if that's not the case, > you > have to provide correct instructions via the command line. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > 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.