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

Dr. Vitaly Chaban vvchaban at gmail.com
Mon Sep 23 10:42:18 CEST 2013

Dear Jonathan -

Is it not a PBC effect? Try to display atoms as spheres - it will look
better. Otherwise, use the options in trjconv to remove PBC in the
visualized structure(s).

Dr. Vitaly V. Chaban

On Mon, Sep 23, 2013 at 9:22 AM, Jonathan Saboury <jsabou1 at gmail.com> wrote:
> 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:
> http://www.sendspace.com/file/gx8j97
> 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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