[gmx-users] Funky output trajectory (lines all over the place)

Jonathan Saboury jsabou1 at gmail.com
Mon Sep 23 09:22:51 CEST 2013

I tried minimizing a box of cyclohexanes and water. The first frame is
fine, but after that seemingly random lines form in vmd with the
cyclohexanes. The waters seem to minimizing just fine though.

I am sure I am just doing something extremely silly and I just don't know
it because of ignorance. I have no formal training on simulations, you are
my only hope!

Perhaps using the em.gro with the em.trr is not the correct way to
visualize? I used the command: "vmd em.gro em.trr"

Or something is wrong with my em.mdp?
em.mdp: http://pastebin.com/raw.php?i=LPPN5xRF

Commands used: http://pastebin.com/raw.php?i=Jk0fKLJj
Here are all the files, in case you need them:

Sorry for dumping all of this, but I am genuinely stuck. I've tried reading
about the mdp file format but i only understand ~5%. If I could have done
more I would have tried :/

Thank you all, it is really appreciated.

-Jonathan Saboury

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