On 5/14/14, 7:54 AM, elham tazikeh wrote:
dear gromacs users i did simulate zinc and copper ion on human growth hormone protein when i saw my md.gro and md.xtc files by VMD software i found out my system isn,t in the box(cubic) i tried to solve this problem by : trjconv -f md.xtc -s md.tpr -o new.xtc -n index.ndx -pbc mol but there is this problem,again. could you please help me
Often times, a single pass of trjconv is insufficient. At the very least, try using the (intuitive) -center option. Otherwise, consult http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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.
