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Kévin Kempfer

Building ethylenic polymers ?

Hi,

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 !

Kevin KEMPFER

PS : Thanks for this useful Polymer Modeler tool.

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    Benjamin P Haley

    Hi Kevin,

       Thanks for your excellent question.  I'm sorry it has taken so long to respond.  We (tool authors) don't always see questions that aren't attached to the tool.  

       PolymerModeler doesn't have an option for your case, but we probably should implement this.  You can submit a wish for a new feature from the tool page.  Other users may also want this, too.

       Sorry we can't help you right now.  Thank you for the very useful feedback.

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      Kévin Kempfer

      Thanks for your reply ! It's better late than never, and I recognize my error posting my question on the general page. I finally made my own code to build my specific polymer melt (but it is not general as yours). I will continue to follow this promising PolymerModeler's evolution. Kevin Kempfer.

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