Vesimulus — Molecular Systemic Simulations

From the documentation:

"Vesimulus is a simulation package for molecular stochastic simulations of metabolic or regulatory biological systems. It was developed because there was no software available which could perform simulations of how the proteins of the bacterial photosynthetic apparatus work in detail. These origins date back to 2005, when Florian Lauck set up the very first version during his bachelor thesis. Since then vesimulus was used to set up a consistent dynamic model of the bacterial photosynthesis including a complete parameterization in another two bachelor theses by Sarah Blass and Xavier Mol and also as a tool and testbed to study how to bridge the gap in scales between computational approaches from the molecular and the systems biological regimes."

Vesimulus was recently used for a systemic parametrization of the bacterial photosynthetic apparatus, in which the results from the molecular-stochastic simulation were compared to a set of macroscopic time-dependent experiments. With this combination we are now able to bridge between the so far essentially unconnected fields of molecular biological and systems biology (published in PLoS ONE).

You can download an archive with the simulation engine with all currently included protein models (mainly from photosynthesis) and the documentation including some tutorials here (version 2.1 of July 2, 2012). To use this software you need an ANSI C++ compiler, the Gnu Scientific Library, and the typical BSD or GNU userland tools. It was developed and tested on a variety of Linux and MacOSX version.

For questions, suggestions, bug reports, or if you are willing to share your protein models with other please contact the main author. If you want to bookmark this page please use

This software is free for academic users. It comes with absolutely no warranty. By downloading or using this software you agree that you are responsible for any consequences (sorry,  but I have to state that). If you want to use vesimulus (or parts thereof) for commercial purposes please contact the author.

The previous version 2.0.3 can be obtained here. The most important changes between 2.0 and the current 2.1 are that the directory layout was cleaned up so that the core parts of the simulation engine are now separated from the proteins and observables. There is one change that may break backwards compatibility: version 2.1 now allows to define and use constants in the setup files. Beyond that the setup file syntax has not changed.

For historians there is an even older version 2.0RC1 available 🙂