Python Simulation Interface for Molecular Modeling

Recent News:    PySIMM version 1.0 release    |    Zeo++ interface in new version 0.2.3    |    Bugfix: v0.2.2   


pysimm is an open-source object-oriented Python package for molecular simulations. It handles data organization for particles, force field parameters, and simulation settings so you can focus on developing your simulation workflow. For a detailed reference document, see the Documentation page.

Force Field Assisted Linear Self-Avoiding Random Walk

Create long linear polymer chains structures modeled with common atomistic force fields. The random walk application in pysimm makes it easy to turn a reference repeat unit into a system of long, linear polymer chains. See the random_walk application section of the reference document for more information.

LAMMPS Integration

pysimm integrates smoothly with LAMMPS for performing large-scale particle based molecular simulations. Although still fully customizable, many simulation parameters are intelligently inferred from a molecular system definition to simplify the simulation setup process. You can choose to prepare raw LAMMPS input files yourself or use pysimm classes to easily set up complex simulation algorithms.

The interaction with software packages uses an abstract object-oriented design that allows simulations to be provided as adjustable parameters for applications. Simulation Python objects can be swapped in and out of application workflows. See the lmps module section of the reference document for more information.

Cassandra Integration

The abstract Simulation architecture has been extended to support simulation with the Cassandra monte carlo software package. Grand canonical monte carlo simulations can be performed on pysimm System objects, enabling iterative Monte Carlo-Molecular Dynamics workflows to study the relaxation of materials upon adsorption of small molecules. See the examples in the source code repository and the documentation for more information.

Support for Common Atomistic Force Fields

pysimm includes parameters for various atomistic force fields in an organized, searchable database that can be programatically used to update topology information for pysimm system structures. Choose to use simple typing rules to assign particle types, or manually choose the appropriate ones. Then let pysimm do the rest of the work, automatically updating bond topologies from the force field database. See the forcefield package section of the reference document for more information.

Integration with dedicated software for geometry analysis

pysimm integrates with two well-renowned tools for structural and topological analysis of molecular systems. Either you prefer to use Zeo++ from Dr. M.Haranczyk or you used to work with Poreblaser developed in Dr. L.Sarkisov's group in both cases you can setup structural analysis of your samples in pysimm in a consistent and fully automated way.

Open Source Development

The source code and development can be viewed at our GitHub repository. pysimm is licensed under the MIT License.

If you use pysimm, please cite:

Funding for this project is provided by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, under Award DE-FG02-17ER16362, as part of the Computational Chemical Sciences Program. Funding for this project was initially provided by the National Science Foundation Grant No. (ACI-1613155).