molecular dynamics to simulate the flow of molten polymers between plates

LAMMPS LAMMPS Mailing List Mirror
1

I would like to use molecular dynamics to simulate the flow of molten polymers between plates, so as to analyze the interfacial properties. I just took over this task, so I’m looking for some ideas from my predecessors.

2

I don’t know how other people build these kinds of simulations.
I’ve been using a combination of these scripts to generate LAMMPS data files for various kinds of polymers:
“moltemplate.sh”,
“genpoly_lt.py”,
“ndmansfield”, and
“interpolate_curve.py”
(Disclaimer: I wrote these tools for this purpose.)

here are some pictures of the results:

http://moltemplate.org/examples/force_fields/index.html#alkane_chain_single
(all-atom polymer with a realistic force field. no walls
tutorial/example files available)

http://moltemplate.org/visual_examples.html#translocation
(walls are made from immobilized atoms, purple.

tutorial/example files available)

http://moltemplate.org/images/prokaryotes/confined_supercoiling_2016-1-13.jpg
(coarse grained DNA model. Cylindrical and spherical walls use “fix wall/region”.
No tutorial files for this example yet.)

http://moltemplate.org/images/prokaryotes/ultrasmall_Luef++Banfield2015_model_2016-9-02.jpg
(Coarse grained DNA model. Walls are made from immobilized atoms, cyan.
No tutorial files for this example yet.)

In most of these examples, the polymers are confined within some kind of container. (Either using “fix wall/region” or using immobilized atoms.) You can run these simulations under conditions of constant volume or constant pressure.

Here are some general instructions that (briefly) explain how to use these different scripts together:
http://moltemplate.org/images/misc/polymers_follow_a_curve.png

http://moltemplate.org/doc/index

https://github.com/jewettaij/ndmansfield/blob/master/doc/docs_ndmansfield.txt

I realize this is not a complete tutorial. If you get stuck on any of these steps, feel free to post a question.

Andrew