SIMONA is freely available for educational use. Contact us if you would like to use it commercially.

To obtain the code or if you have further questions, please write to wolfgang.wenzel∂kit.edu.

 You can find the preprocessor documentation here

Strunk T, Wolf, M. et al. SIMONA 1.0: an efficient and versatile framework for stochastic simulations of molecular and nanoscale systems. J Comput Chem 33, 2602–2613 (2012).

SIMONA 1.0 ACADEMIC LICENSE AGREEMENT, VERSION 2.2, July 2012 between Karlsruhe Institute of Technology, Kaiserstr. 12, 76131 Karlsruhe, Federal Republic of Germany (subsequently referred to as “KIT”) and Licensee on the software system SIMONA Version 1.0 (subsequently referred to as „Software“) developed by Prof. Wenzel PhD at Institute of Nanotechnology (INT) Nanoscale and Biomolecular Simulation Group Phone: +49-721-608-26386, e-mail: wolfgang.wenzel at kit.edu (subsequently referred to as “contact person”) for non-commercial use subject to the following conditions: §1 GRANT OF LICENSE: Licensee guarantees, that he is a non profit research institution. Taking this in consideration KIT grants, and Licensee hereby accepts, a non-exclusive, non-transferable, royalty-free and revocable right to use the Software for non-commercial use and academic purposes to the extent of its rights and in accordance with the terms of this Academic License Agreement. §2 NON-COMMERCIAL USE: (1) Licensee shall not use the Software or any results produced with the Software for commercial purposes of any kind. (2) Licensee shall not use the Software or any results produced with the Software in connection with the provision of consultancy, modeling or other services, whether for value or otherwise, on behalf of any third party. (3) Licensee shall not use the Software to write other software that duplicates the functionality of the Software. (4) Licensee shall not rent, lease, sublicense or otherwise sublet the Software or any results produced with the Software to third parties. (5) §2(1), §2(2), §2(3) and §2(4) apply as well to any modifications, extensions, derivatives and parts of the Software. §3 COPIES OF THE SOFTWARE: (1) The licensed copy of the Software shall only be installed and used on computers at Licensee’s site by Licensee and members of Licensee’s organization at Licensee’s site who have read and agreed with this license. Licensee shall make only such copies of the Software which are necessary to install and use it as permitted by this Academic License Agreement, or are for purposes of backup and archival records. (2) Licensee shall take all reasonable steps to prevent unauthorised use or copying of the Software by third parties. (3) The Licensee shall inform KIT if the original or any copy of the Software is lost or if it is discovered that any third party has possession of any part of the Software by unauthorised means. (4) Licensee shall not distribute copies of the Software to third parties or to others outside of Licensee’s site. Instead refer such third parties to KIT, the contact person and the Internet page of the Software. §4 BUGS AND IMPROVEMENTS: Licensee shall agree to inform KIT or the contact person of any failures detected in the Software in particular weak points and/or where improvements are needed in the functionality and/or user interface and of possibilities for improving them. KIT encourages Licensee to contribute patches/improvements back to KIT and the contact person. §5 OWNERSHIP: The ownership of the Software is protected by the copyright law of the Federal Republic of Germany. KIT is the owner of all economic rights and copyright exploitations rights (so called “vermögensrechtliche Befugnisse”, see German UrhG §69b) of the Software. §6 LICENSEE’S MODIFICATIONS AND DERIVATIVE WORKS: (1) Licensee may modify the Software and may use it to create derivative works for Licensee’s internal use only at Licensee’s site covered by this Academic License Agreement. (2) Licensee shall not distribute such modified or derivative software to others outside of Licensee’s site without written permission of KIT. (3) If Licensee wants that Licensee’s modifications of the Software will be available in subsequent releases of the Software and thus to third parties, Licensee shall agree to allow KIT to integrate Licensee’s modifications into subsequent releases of the Software and thus agree that Licensee’s modifications shall become part of the Software. Hereby Licensee grants to KIT a non exclusive, royalty-free, sublicensable right to use such modifications for each type of use. (4) If Licensee’s modifications are essential improvements of the functionality of the Software, KIT is willing to negotiate and conclude a separate license agreement with Licensee to remunerate Licensee appropriately for an assignment as described in §6(3). §7 PUBLICATIONS: Licensee shall be obliged to acknowledge in an appropriate manner KIT, Institute of Nanotechnology (INT), the Nanoscale and Biomolecular Simulation Group and the contact person when publishing results based on the Software, even after the Software has been modified. §8 TERMINATION: (1) KIT may terminate this Academic License Agreement with immediate effect by written notice (or by e-mail) to Licensee if Licensee continues to be in serious or continuous breach of any of its obligations hereunder and fail to cure the same within 30 days of written notice or notification by e-mail specifying such breach. (2) Upon termination Licensee shall immediately cease using the Software and shall return or destroy all copies including file saves of the Software, documentations and other accompanying materials and shall declare this in writing to KIT within one month after termination. (3) After the termination of this Academic License Agreement the obligations in §2 particularly (5), §3(3), §3(4), §5, §6(3), §7, §8(2), §9, §10 and §11 will continue to be effective. §9 WARRANTY: There is no warranty for the Software, to the extent permitted by applicable law. KIT provides the program "as is" without warranty of any kind, either expressed or implied, including, but not limited to the fitness for a particular purpose. The entire risk as to the quality and performance of the Software, as to the results obtained from the Software and as to any use made of the results is with Licensee. §10 LIABILITY: (1) Except for cases of intent or gross negligence, KIT shall not be liable to Licensee for any damage in conjunction with the Software or failures of the Software and KIT shall not be liable for any direct, indirect or consequential loss or damage, such as, but not limited to, loss of profit and loss of revenue, due to the use of the Software. (2) Except for cases of intent or gross negligence, KIT shall not be liable to Licensee for legal defects of the Software or possible claims of third parties. At the moment, KIT is not aware of any claims enforced by third parties against the use of the Software. (3) Licensee shall be liable for any loss, damage or injury to third parties resulting from Licensee’s utilization of the Software in whole or in part. Licensee will indemnify and hold harmless KIT and its employees from and against any third party claims in connection with Licensee’s utilization of the Software. (4) The Licensee shall be liable for any damages or losses KIT and its employees may suffer arising from unauthorised copying or disclosure of the Software including but not limited to all direct, indirect and consequential losses. §11 JURISDICTION AND APPLICABLE LAW: Any disputes arising from or in connection with this Academic License Agreement, which cannot be solved amicably, shall be referred to the court located at the seat of KIT. The applicable law shall be that of the Federal Republic of Germany. §12 COMMERCIAL LICENSE: Alternatively to this Academic License Agreement, KIT offers a license to use the Software commercially as well, on the basis of a commercial license agreement. If Licensee is interested in such a license please contact KIT, Institute of Nanotechnology (INT), the Nanoscale and Biomolecular Simulation Group and the contact person. §13 Micellaneous: KIT is the owner of the US-patent US2011/0218788A1 and the corresponding EP patent application EP2363820A1 “Method and system for determining the solvent accessible surface area and its derivates of a molecule”. This method is implemented in SIMONA.