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

Mark Abraham mark.j.abraham at gmail.com
Mon Sep 23 15:36:17 CEST 2013

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


> 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
> 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
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

More information about the gromacs.org_gmx-users mailing list