I'm trying to perform ab-initio MD on polymer system.

I've built single chain of polycarbonate (PC) with the length of ~40 angstroms and now I'm building initial configuration. I've calculated how much of this chains are needed to achieve the experimental density of PC and tried to pack it with Packmol in cube 50x50x50 angstroms.

It fails to make good enough packing, so what are the usual protocols to pack polymer system to experimental density?

  • $\begingroup$ Have you tried this tool by any chance: nanohub.org/tools/polymod (Polymer Modeler) $\endgroup$
    – Greg
    Mar 13, 2021 at 19:46
  • 5
    $\begingroup$ from a colleague who worked on this: "40 A is pretty big in a 50 A cube, the software PACKMOL packs at random so you probably won't get packing with those dimensions. You should pack enough polyC for 50 cubic A into a larger volume and run NPT simulations to compress it down to 50 cubic A." $\endgroup$
    – Cody Aldaz
    Mar 13, 2021 at 22:28
  • 3
    $\begingroup$ What Cody said, make a bigger box, and use NPT simulation to compress it down. PACKMOL also packs things a little funny sometimes, and this would help avoid this.... none of that matters if you do a proper equilibration. $\endgroup$
    – B. Kelly
    Mar 14, 2021 at 7:06

1 Answer 1


Finally, I just used simulated annealing of NPT ensemble: heated it above glass transition temperature and cooled back down. It equilibrated to the density very close to experimental.

Hope my experience will help someone.

UPD: Equilibrating the system at very high pressure (I used 1000 bar) also work fine in difficult cases.

  • $\begingroup$ +1 Thanks for coming back and sharing your update with us! It's a lot more helpful to future users than just leaving the question unanswered. I'll mention that putting the green checkmark there only gains you points if you put it on someone else's answer, so all it's doing right now is discouraging others from adding additional answers (which might not be a bad thing, I'm just mentioning it in case you didn't know). $\endgroup$ Mar 22, 2021 at 16:50
  • $\begingroup$ @NikeDattani ok, I didn't know how it works. $\endgroup$
    – Roman
    Mar 23, 2021 at 2:26
  • $\begingroup$ Just a word of warning - a simulation result being close to experiment does not make it a correct simulation :) $\endgroup$
    – B. Kelly
    Jan 12, 2022 at 2:39

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