2008/07/15 by Michael Grünwald, M. Grünwald, Christoph Dellago +3 · 2 citations
Biochemistry, Genetics and Molecular Biology · Engineering · Physics and Astronomy · #Phase Equilibria and Thermodynamics #Protein Structure and Dynamics #Spectroscopy and Quantum Chemical Studies #cond-mat.stat-mech
paper · pdf · doi:10.1063/1.2978000
9 pages, 12 figures, submitted to J. Chem. Phys
arxiv created 2008/07/15 · openalex publication_date 2008/11/17 · arxiv updated 2009/12/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
The kinetics of collective rearrangements in solution, such as protein folding and nanocrystal phase transitions, often involve free energy barriers that are both long and rough. Applying methods of transition path sampling to harvest simulated trajectories that exemplify such processes is typically made difficult by a very low acceptance rate for newly generated trajectories. We address this problem by introducing a new generation algorithm based on the linear short time behavior of small disturbances in phase space. Using this "precision shooting" technique, arbitrarily small disturbances can be propagated in time, and any desired acceptance ratio of shooting moves can be obtained. We demonstrate the method for a simple but computationally problematic isomerization process in a dense liquid of soft spheres. We also discuss its applicability to barrier-crossing events involving metastable intermediate states.