KIMMDY – a hybrid approach for Molecular Dynamics (MD) simulation
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
HITS, the Heidelberg Institute for Theoretical Studies, was established in 2010 by 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, mathematical, and computer sciences. Major research directions include complex simulations across scales, making sense of data, and enabling science via computational research. Application areas range from molecular biology to astrophysics. An essential characteristic of the Institute is interdisciplinarity, implemented in numerous cross-group and cross-disciplinary projects. The base funding of HITS is provided by the Klaus Tschira Foundation.
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