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.
