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

[Justin Lemkul]

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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================