Analyzing Interfaces, Interactions and Self-Assembly in Soft Matter Simulations with PySoftK

12 April 2024, Version 1
This content is a preprint and has not undergone peer review at the time of posting.


Molecular dynamics simulations have become an essential tool in the study of soft matter and biological macromolecules. The large amount of high-dimensional data produced by such simulations does not immediately elucidate the atomistic mechanisms that underlie complex materials and molecular processes. Analysis of these simulations is complicated: the dynamics intrinsic to soft matter simulations necessitates careful application of specific (often complex) algorithms to extract meaningful molecular scale understanding. There is an ongoing need for high-quality computational workflows to facilitate this analysis in a reproducible manner with minimal user input. In this work, we introduce a series of new computational tools for analyzing soft matter interfaces, molecular interactions (including ring-ring stacking), and self-assembly. In addition, we include a number of auxiliary tools, including a useful function to unwrap molecular structures that are greater than half the length of their corresponding simulation box. These tools are contained in the PySoftK software package, making application of these algorithms straightforward for the user. These new simulation analysis tools within PySoftK will support high-quality, reproduce analysis of soft matter and biomolecular simulations to bring about new predictive understanding in nano- and biotechnology.


molecular dynamics simulations
analysis codes
intrinsic surfaces
soft matter
biological molecules

Supplementary materials

Supplementary Information
Theoretical explanations of Graph Theory in our implementation, concrete examples, and PySoftK code snippets for hands-on practice are included in the ESI.


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