From: Sourav Ray (
Date: Wed Sep 16 2015 - 04:34:43 CDT


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

Can someone please suggest any remedial action so that I may extract normal
bond visualizations after the necessary processing.

Thanks and regards
Sourav Ray