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 .
- 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, please see the Detailed Description section. Every function is explained in the detailed description section.
- An explanation of basic Terms can be found here .
- SIMONA papers
- For background information see Papers related to POEM++ here.
For information how to modify this documentation click here.