From: conor parks (
Date: Wed Sep 16 2015 - 11:59:14 CDT

If I understand your issue correctly, changing the drawing method from
lines to dynamic bonds should do the trick.


On Wed, Sep 16, 2015 at 5:34 AM, Sourav Ray <> wrote:

> Hello
> After running simulation of a peptide molecule for 30ns (2fs times steps)
> under periodic box and NVT conditions. Upon unwrapping the atoms, I am
> getting bonds between certain atoms as elongated lines, the probable reason
> being one atom of the bond is in one periodic box and the other in the next
> one.
> Can someone please suggest any remedial action so that I may extract
> normal bond visualizations after the necessary processing.
> Thanks and regards
> Sourav Ray

B.S.E in Chemical Engineering, University of Michigan, 2012
PhD candidate in Chemical Engineering, Purdue University