KIMMDY – a hybrid approach for Molecular Dynamics (MD) simulation

5. July 2021

The simulation scheme called KIMMDY (Kinetic Monte Carlo / Molecular Dynamics) enables covalent bond breakages in all-atom Molecular Dynamics (MD) simulations. The bond rupture rates are calculated based on the interatomic distances in the MD simulation and then serve as an input for a Kinetic Monte Carlo step. This hybrid approach allows to study breakages in large molecular systems (like the structural protein collagen) bridging various time scales between MD and the rupture processes.

KIMMDY was developed by the Molecular Biomechanics (MBM) group at HITS. The code and some example files can be found on GitHub.

References:

Paper: Hybrid Kinetic Monte Carlo / Molecular Dynamics Simulations of Bond Scissions in Proteins
Benedikt Rennekamp, Fabian Kutzki, Agnieszka Obarska-Kosinska, Christopher Zapp, and Frauke Gräter
Journal of Chemical Theory and Computation

Example: https://www.h-its.org/projects/mechanoradicals-in-collagen/

About HITS

The Heidelberg Institute for Theoretical Studies (HITS) was established in 2010 by the physicist and SAP co-founder Klaus Tschira (1940-2015) and the Klaus Tschira Foundation as a private, non-profit research institute. HITS conducts basic research in the natural sciences, mathematics and computer science, with a focus on the processing, structuring, and analyzing of large amounts of complex data and the development of computational methods and software. The research fields range from molecular biology to astrophysics. The shareholders of HITS are the HITS-Stiftung, which is a subsidiary of the Klaus Tschira Foundation, Heidelberg University and the Karlsruhe Institute of Technology (KIT). HITS also cooperates with other universities and research institutes and with industrial partners. The base funding of HITS is provided by the HITS Stiftung with funds received from the Klaus Tschira Foundation. The primary external funding agencies are the Federal Ministry of Education and Research (BMBF), the German Research Foundation (DFG), and the European Union.

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