On 9/28/14 9:14 AM, Anurag Dobhal wrote:
Hey gromacs users I got the confout.gro file by running the command mdrun -v -deffnm em -o confout.gro and then i ran the command " perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat " but now the teminal says that Reading..... Use of uninitialized value $box_x in multiplication (*) at inflategro.pl line 339. Use of uninitialized value $box_y in multiplication (*) at inflategro.pl line 340. Scaling lipids.... There are 0 lipids... Illegal division by zero at inflategro.pl line 380 is this output is expected ???
No, fatal errors like that are not expected. If EM successfully completed and wrote a confout.gro file, there should be no problem. Visualize confout.gro and make sure its contents are sane.
-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.
