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

2013-09-23 Thread Jonathan Saboury
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.

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

2013-09-23 Thread Dr. Vitaly Chaban
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 jsab...@gmail.com wrote: I tried minimizing

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

2013-09-23 Thread Mark Abraham
On Sep 23, 2013 9:23 AM, Jonathan Saboury jsab...@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