[gmx-users] Unable to visualize my Polymer chains in VMD software generated using RIS theory in a proper way

[Abhishek Gupta]

Dear GROMACS Users,

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