Home

Welcome to the polymer-libraries wiki!

Polymer-libraries come with the intent of collecting some useful routine to analyze the so called "beaded chains". In molecular dynamics a beaded chain is a chain made of points with a given potential (usually Lennard-Jones) attached, consecutively, to form a chain. Such chains can be open or closed (rings) in simple cases. They can also form complex topologies. The idea behind this library is to have some routine to calculate useful information about such chains, like:

• radius of gyration,
• contact probability between given points or between every element,
• end to end distance,
• writhe
• twist (in this case we require a more complex model than a beaded chain)
• accessible surface area
• Alexander polynomials (to identify knots)
• and more.

The routines were developed to solve the problems that were arising during my project and so they may have a particular format for the data and some assumption regarding the indexing of the beads. The trajectories that I usually use and for which this code was developed were obtained with "HooMD-Blue". The assumptions used to develop the routine will be explained in the wiki.