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! -- 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].
