On 3/20/15 8:48 PM, Jonathan Saboury wrote:
Dear all, I ran an energy minimization and molecular dynamics on biotin in a box of water. The EM ran fine however the MD output shows biotin broken into pieces from the start to the end. Did the MD run correctly? I used the trjconv with the "-pbc nojump" flag, so I am not sure why it is showing it in pieces. Useful files: Commands Used: http://pastebin.com/raw.php?i=tafLnpS1 em.mdp: http://pastebin.com/raw.php?i=499VtVLY md.mdp: http://pastebin.com/raw.php?i=mgGZBDC2 ALL FILES (41 MB): http://ge.tt/api/1/files/32E9udC2/0/blob?download Pictures of VMD visualization: em end: http://oi60.tinypic.com/14mfcwg.jpg md start (should be same as em end, but isn't): http://oi59.tinypic.com/ixbkue.jpg md end: http://oi60.tinypic.com/nbrb87.jpg I need the visualization to look nice so I can present it to my PI. Thank you!
Using -pbc nojump doesn't make molecules whole. Using -pbc whole or -pbc mol does. trjconv -pbc mol -center should be all you need -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 [email protected] | (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 [email protected].
