Welcome to openmm-lib’s documentation!

This is a wrapper to OpenMM designed to run and analyze polymer simulations (Brownyan dynamics).

You can use this library if:

-You need to run a coarse-grained polymer simulation -You have equally sized monomers -You need to have ability to make monomers transparent -You want a fast and efficient way to calculate things like Rg(s) and Pc(s) (Pc - contact probability) -You want to deal with knot complexity (Alexander’s polynomial) or linking number -You want to analyze contact maps -You want to make cool pictures in pymol -You want to replicate simulations from the Mirnylab papers.

The main library, openmmlib, is a class to perform simulations.

A file knotAnalysis.py contains code needed to calculate Alexander’s polynomials, a measure of knot complexity. It also uses OpenMM to help unwrap polymer and reduce time needed to calculate Alexander’s polynomial

A file polymerScalings.py has some utilities to calculate Rg(s) and Pc(s) for polymer conformations in a fast and efficient way.

A file contactmaps.py has code to quickly calculate contacts within a polymer structure, and organize them as contactmaps. It is used by polymerScalings.

A file pymol_show has utilities to visualize polymer conformations using pymol

Contents:

Indices and tables

Table Of Contents

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