Rapid Exploration of Configuration Space with Diffusion Map-directed-Molecular Dynamics
Identifieur interne : 000298 ( Main/Merge ); précédent : 000297; suivant : 000299Rapid Exploration of Configuration Space with Diffusion Map-directed-Molecular Dynamics
Auteurs : Wenwei Zheng ; Mary A. Rohrdanz ; Cecilia ClementiSource :
- The journal of physical chemistry. B [ 1520-6106 ] ; 2013.
Abstract
The gap between the timescale of interesting behavior in macromolecular systems and that which our computational resources can afford oftentimes limits Molecular Dynamics (MD) from understanding experimental results and predicting what is inaccessible in experiments. In this paper, we introduce a new sampling scheme, named Diffusion Map-directed-MD (DM-d-MD), to rapidly explore molecular configuration space. The method uses diffusion map to guide MD on the fly. DM-d-MD can be combined with other methods to reconstruct the equilibrium free energy, and here we used umbrella sampling as an example. We present results from two systems: alanine dipeptide and alanine-12. In both systems we gain tremendous speedup with respect to standard MD both in exploring the configuration space and reconstructing the equilibrium distribution. In particular, we obtain 3 orders of magnitude of speedup over standard MD in the exploration of the configurational space of alanine-12 at 300K with DM-d-MD. The method is reaction coordinate free and minimally dependent on a priori knowledge of the system. We expect wide applications of DM-d-MD to other macromolecular systems in which equilibrium sampling is not affordable by standard MD.
Url:
DOI: 10.1021/jp401911h
PubMed: 23865517
PubMed Central: 3808479
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