On 6/19/15 1:35 PM, John Degenstein wrote:
Hello, I am trying to build a bigger liquid phase (1000) from a small cluster of molecules (125). So far I have succeeded in forming the small cluster of 125 molecules shown in the below image. This was after running gmx trjconv ... -pbc cluster -center to bring the molecules into the middle of the box. http://i.imgur.com/nlgDUzh.png Now, the seemingly very trivial issue I am having is that I cannot figure out how to remove the empty space surrounding the cluster. I would like to do this automatically rather than by manually specifying a box size. Can anyone suggest a workflow for doing this?
Determining the box size from maximum and minimum coordinates along each axis should be simple from the coordinate file, otherwise apply a position restraint and run a couple of steps of NPT and the box will shrink down to fit the system.
-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.
