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Optimizing molecular models through force-field parameterization via the efficient combination of modular program packages

 
: Hülsmann, Marco; Kirschner, Karl N.; Krämer, Andreas; Heinrich, Doron D.; Krämer-Fuhrmann, Ottmar; Reith, Dirk

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Snurr, R.Q.:
Foundations of Molecular Modeling and Simulation : Select Papers from FOMMS 2015, Conference on Foundations of Molecular Modeling and Simulation, July 12-16, 2015, Portland, Oregon, USA
Singapore: Springer Science+Business Media, 2016 (Molecular Modeling and Simulation)
ISBN: 978-981-10-1126-9 (Print)
ISBN: 978-981-10-1128-3 (Online)
S.53-77
Conference on Foundations of Molecular Modeling and Simulation (FOMMS) <6, 2015, Portland/Or.>
Bundesministerium für Bildung und Forschung BMBF
01IH13005B; SkaSim
Englisch
Konferenzbeitrag
Fraunhofer SCAI ()
molecular modeling; force field; numerical optimization; high performance computing; modular software packages

Abstract
A central goal of molecular simulations is to predict physical or chemical properties such that costly and elaborate experiments can be minimized. The reliable generation of molecular models is a critical issue to do so. Hence, striving for semiautomated and fully automated parameterization of entire force fields for molecular simulations, the authors developed several modular program packages in recent years. The programs run with limited user interactions and can be executed in parallel on modern computer clusters. Various interlinked resolutions of molecular modeling are addressed: For intramolecular interactions, a force-field optimization package named Wolf2Pack has been developed that transfers knowledge gained from quantum mechanics to Newtonian-based molecular models. For intermolecular interactions, especially Lennard–Jones parameters, a modular optimization toolkit of programs and scripts has been created combining global and local optimization algorithms. Global optimization is performed by a tool named CoSMoS, while local optimization is done by the gradient-based optimization workflow named GROW or by a derivative-free method called SpaGrOW. The overall goal of all program packages is to realize an easy, efficient, and user-friendly development of reliable force-field parameters in a reasonable time. The various tools are needed and interlinked since different stages of the optimization process demand different courses of action. In this paper, the conception of all programs involved is presented and how they communicate with each other.

: http://publica.fraunhofer.de/dokumente/N-399825.html