Date: Tue Mar 15 2016 - 01:17:07 CDT

Hello VMD Users,

This is a repost of my question that i posted on 12th March.

I am trying to visualize the simple polyethylene chains (multiple chains)
consisting of certain number of atoms generated using RIS theory using VMD.
I'm using the PDB format to express coordinates to visualize my chains.

VMD is showing bonds between the atoms of the polyethylene chains which are
quite close to each other and are not connected in succession. Example:
ATOM NO 4 connected to ATOM NO 25 by a bond, ATOM NO 8 connected to ATOM NO
18 and many such cases.

What might be the possible cause of this unusual visualization in VMD ?
Does VMD connects Atoms taking in some distance criterion ? Can we change
that distance criteria that VMD utilize to connect the atoms of a polymer
chain ?

KIndly answer

Thanks and Regards
Abhishek Kumar Gupta