A collection of demos, vignettes, and tutorials for the polymerist package for polymer structure generation and molecular dynamics (MD) simulation preparation (https://github.com/timbernat/polymerist)
First, create a local clone of this repository in the directory of choice by running:
git clone https://github.com/timbernat/polymerist_examples
cd polymerist_examplesNext, follow the installation instructions in the polymerist install docs to set up a conda environment which includes the polymerist package
At this point, you should be good to go and try out the examples!
Series 1 - Building polymers
- 1.1 - Introduction: nylon polymers
- 1.2 - Simple vinyl polymers and autopolymerization
- 1.3 - Kapton polyimides and with multiple intermonomer bonds
- 1.4 - Crosslinkable MPD-TMC polyamides
- 1.5 - PEG-PLGA block copolymers
- 1.6 - Conjugated thiophenyl polymers with arbitrary sidechains
Series 2 - Preparing systems containing polymers
- 2.1 - Loading a polymer structure into OpenFF
- 2.2 - Polymer metadata and partial charge assignment
- 2.3 - Solvation and packing of polymer melts
- 2.4 - Reduction Charge Transfer (RCT) for generating custom library charges
Series 3 - Running polymer simulations
- 3.1 - Exporting polymer systems to common MD engines
- 3.2 - Reproducibly serializing OpenMM simulations
- 3.3 - Running series of OpenMM simulations
- 3.4 - Start-to-finish polymer simulation workflow for an ATRP polymerization
Series 4 - Miscellaneous
Feel free to email timotej.bernat@colorado.edu for questions or requests for more examples.