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Shyno Mathew

missing bonds

Hi I am trying to generate a polystyrene structure. Initially I was aiming for a single chain with 20 monomers. But once I loaded the lammps data file in vmd, I saw some bonds were missing. To better understand the issue I did 2 test simulations: 1. single chain 1 monomer simulation The lammps data file showed:

18 atoms 17 bonds 26 angles 28 dihedrals 4 impropers

3 atom types 5 bond types 2 angle types 3 dihedral types 1 improper types

once I load this in vmd, I can see a C-C bond (8-13)in the benzene ring is missing.

2. single chain 2 monomers: The lammps data file showed:

34 atoms 33 bonds 52 angles 65 dihedrals 8 impropers

3 atom types 5 bond types 2 angle types 3 dihedral types 1 improper types

in this case there is a twist, in vmd I see two bonds (8-13, 24-29) are missing even though the above information suggests only one is missing. is there any way to solve this issue. Since I need to go for higher chain lengths it is hard to include bonds manually. Also could you please confirm the angles, dihedrals are correct as well. Thanks Shyno Mathew

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    Benjamin P Haley

    Hi! Sorry for the long delay in responding to your question. I believe this problem is fixed in version 2.1 of PolymerModeler, which is about to be deployed.

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