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

[Mark Abraham]

On Sep 23, 2013 9:23 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!

Google is pretty useful, too ;-)
http://www.gromacs.org/Documentation/FAQsdeals with this kind of
issue.

Mark

> 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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