Building ethylenic polymers ?
I am trying to use Polymer Modeler to build initial amorphous MD configurations of 1,4-cis-polybutadiene, which entail both single and double carbon-carbon bonds in its backbone.
I uploaded my monomer and I am able to build polymer chains. My issue is that I am not able to randomize the torsion angles between each single carbon-carbon bonds. In the "configuration" tab, either I have to choose the option "apply only to torsions between monomers" or "apply to all torsions in backbone". On the one hand, I only allow 1/3 of my single carbon-carbon bond to rotate ; on the other hand, I loose my "cis" stereochemistry. The best would be to allow all torsions with covalent torsion energies sp3-sp3 and sp2-sp2 for the single and double bonds, respectively, but it looks like such a choice has not been implemented. Maybe there is also something to do with the monomer arrangements in the "monomer structures" tab.
Any clue ?
In advance, thanks a lot for all your advices !
PS : Thanks for this useful Polymer Modeler tool.