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I'm thinking of running MD simulation of poling process (heating and cooling in external electric field) of host-guest polymer system: organic chromophore in polymer matrix (PMMA or polycarbonate).

So, I'm trying to find how to build the system. I've found that Packmol can be used to randomly place prebuilt polymer chains but I don't understand how can I introduce my chromophore (I also need to control polymer density and chromophore weight content).

What tools can you recommend for building such systems and feeding them to some MD code (at the moment I'm considering GROMACS, LAMMPS or CP2k, but I'm not sure)?

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At the moment I have a workflow like this:

  • I draw my structures,
  • generate geometry with Avogadro,
  • build the topology using PolyParGen and LigParGen, and
  • assemble the system using genconf and insert-molecules tools from Gromacs.

It's not perfect, but it works.

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  • $\begingroup$ Tanks for sharing that with us. By the way is that a new workflow you developed after March 4th, or was that already your workflow at the time of asking the question? $\endgroup$
    – Nike Dattani
    Mar 23, 2021 at 14:59
  • $\begingroup$ I've developed it after the question was asked. I've read couple of papers, and tried to eliminate the use of proprietary software. $\endgroup$
    – roma ichenko
    Mar 24, 2021 at 8:17

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