On 9/30/15 12:15 PM, Ebert Maximilian wrote:
Dear list, I am trying to add n-number of molecules in my prepare protein+water+ions box but keep a minimum distance of 1 nm in all directions between the newly inserted molecules. On top of that I want to replace solvent molecules with the newly added molecules. So basically I am looking for gmx genion with the -rmin flag for non ions. Which tool could I use?
No GROMACS tool will do this. You can use gmx insert-molecules in concert with a positions.dat file (with pre-computed locations for the molecules), followed by gmx solvate.
-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.
