Scalable Software Services for Life Science

SIMONA

SIMONA is a generalized simulation kernel and a specific simulation preprocessor, which enables rapid prototyping of forcefields and simulation methods for efficient Monte Carlo simulations. As of now SIMONA could conduct crystal formation simulations, simulate protein folding, protein-protein interactions and conduct protein-ligand docking studies. It is written in a modular manner to allow efficient code reuse for both the developer and the user of the program. The first thing you should do is read the Installation Guide .The SIMONA Preprocessor is divided in several parts, which relate to the type of simulation:

  • POEM++ creates protein Monte Carlo simulations.
  • FlexScreen creates Monte Carlo docking simulations.
  • Generic Monte Carlo creates general molecule Monte Carlo simulations.
  • Setting/Tools contains numerous overall settings for the preprocessor. Some useful Tools can be found here as well.

Installation Guide

To get to know how to install SIMONA, please read the Installation Guide.

Tutorials

If you are using SIMONA the first time, please look through our collection of Tutorials and Guides

 

Description of the settings and expert-settings of SIMONA

If you are looking for information about advanced settings, every function is explained in the detailed description section.

Terminology

An explanation of basic Terms can be found here.

SIMONA papers

For background information see Papers related to POEM++ here.