Welcome to polymerist’s documentation!
This is the documentation for the Polymer-Oriented LibrarY of Monomer Expression Rules and In-silico Synthesis Tools, or just “polymerist” for short.
Polymerist is a unified set of tools for setting up molecular dynamics simulations of general organic polymer systems. It was originally developed around concepts introduced in our manuscript [“Parameterization of General Organic Polymers within the Open Force Field Framework” , Davel, Connor M., Bernat, Timotej, Wagner, Jeffrey R., and Shirts, Michael R.], but has over time evolved into a more fully-featured library.
Features
Generating chemical information-rich monomer residue templates
Enumeration of all possible repeat units of a polymer ensemble given initial monomers and a target polymerization mechanism
Building of linear homopolymers and copolymers (both topologies and coordinates)
Solvating polymer systems
Packing of many polymer chains into melt-like boxes
Force-field parameterization within the OpenFF framework
Interfaces to semi-empirical and graph neural network-based atomic partial charge assignment
Reproducible simulation specification API
Interfaces to OpenMM for running serial simulations with different thermodynamic parameters
Much more!
Getting started: