On 9/3/15 4:57 AM, Martin Nors Pedersen wrote:
Thank you for the reply Justin! I'm sorry for being so naive, but I still cannot get it to work. Trying to follow the procedure described in you link, I got the following message: ______________________________ GROMACS: gmx genbox, VERSION 5.0.4 Executable: /sware/exp/gromacs/5.0.4/bin/gmx_mpi Library dir: /sware/exp/gromacs/5.0.4/share/gromacs/top Command line: gmx_mpi genbox -f lysBox.gro -o lysUrea.gro -ci urea.gro -nmol 300 This tool has been removed from Gromacs 5.0. Please see http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0 for ideas how to perform the same tasks with the new tools. ______________________________ The link in the software message above mentions that "insert-molecules" should be used instead, but that is the library/package that I could not get to work yesterday :S Can anyone help?
The syntax is identical, just replace "genbox" with "insert-molecules." The functionality has literally just been split from genbox, which was trying to do too many things for a simple program. Your command wasn't working before because you were trying to add urea after water, which won't work.
-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.
