From: Norman Geist (
Date: Wed Mar 16 2016 - 04:56:34 CDT

If VMD doesn’t get any bond information from any input file, it will guess bonds for visualization purpose. This guessing is done based on elements vdw radii but before the elements are guessed from atom names, if also this information is not available. If you have overlapping polymers which VMD should not show to be bonded, you need to tell VMD where to draw the bonds. This can be done from the TCL interface or by passing a suitable parameter file, which describes your system e.g. prmtop or psf. Unfortunately VMD doesn’t care about either the connectivity table in PDB files nor the TER lines.


Norman Geist


Gesendet: Mittwoch, 16. März 2016 08:35
An: Norman Geist <>
Betreff: Re: vmd-l: Unable to visualize my polymer chains generated using RIS theory using VMD properly


What do you mean by saying "Proper bond information" ?

KIndly clarify

I was giving the bond connectivity information at the lower of the PDB file to show the connectivity.

Is this problem due to steric hindrance of the non-bonded atoms in polyethylene chain ? Does VMD chose some distance criterion to connect atoms ?




On Tue, Mar 15, 2016 at 1:23 PM, Norman Geist < <> > wrote:

If the atoms are that close, you won’t get any reasonable bond guessing at all. You may want to supply a parameter file to VMD which contains the proper bond information.



Norman Geist


Von: <> [ <> ] Im Auftrag von ABHISHEK GUPTA
Gesendet: Samstag, 12. März 2016 04:10
An: <>
Betreff: vmd-l: Unable to visualize my polymer chains generated using RIS theory using VMD properly



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. The chains are very random and at some points multiple atoms of a chain comes very near to each other. Sometimes, even there is inter chain overlapping and multiple atoms of different chains comes in close vicinity of each other. In such a situation, while visualizing via. VMD, there appears a bond between those close or very close atoms within a chain or between two chains. Therefore, the visulaization by VMD shows that number of bonds is much greater than the number of atoms and forms a cage like structure (in some cases) between the closely spaced or overlapping atoms. What might be the possible cause of this ? 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 in succession ?

Thanks and Regards

Abhishek Kumar Gupta