[gmx-users] Did this MD simulation run correctly? If so, how do I visualize it nicely?

[Jonathan Saboury]

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!