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Jungkyu Park

error during equalization with polyethylene structure

Hi,

I tried to model a polyethylene structure(50 monomers and 15 chains). I used mostly default settings. but while I am running the NVT equailization (I changed the timestep into 1 femtosecond) I keep getting errors. And they are mostly “missing bonds” or “missing atoms” errors. I think there could be a few reasons for this. One possibility is that the initial structure created by polymer modeler is not that good. Or there could be something wrong when the polymer modeler calculate bondings while it makes the Lammps input data file from the initial structure. I tried several different things such as changing timestep or temperature settings, or changing some factors during making initial structure. But they were not that helpful. Do you have any idea to solve this problem?

Thank you

  1. equilization
  2. polyethylene
  3. tool:polymod

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    Benjamin P Haley

    Hi,

    Thanks for your question, and for using this tool. The problem is that the initial structure needs to be relaxed before running MD in LAMMPS. We have a new version of the tool which is almost ready to deploy, which resolves this problem. Sorry for the delay in answering your question.

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    Benjamin P Haley

    I believe that these issues are addressed with the new 2.0 release of PolymerModeler.

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