| Autor: |
Burgin T; Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States., Ellis S; The Molecular Sciences Software Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24060, United States.; Department of Chemistry, Virginia Tech University, Blacksburg, Virginia 24061, United States., Mayes HB; Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States. |
| Abstrakt: |
Transition path sampling methods are powerful tools for studying the dynamics of rare events in molecular simulations. However, these methods are generally restricted to experts with the knowledge and resources to properly set up and analyze the often hundreds of thousands of simulations that constitute a complete study. Aimless Transition Ensemble Sampling and Analysis (ATESA) is a new open-source software program written in Python that automates a full transition path sampling workflow based on the aimless shooting algorithm, streamlining the process and reducing the barrier to use for researchers new to this approach. This introduction to ATESA includes a demonstration of a complete transition path sampling process flow for an example reaction, including finding an initial transition state, sampling with aimless shooting, building a reaction coordinate with inertial likelihood maximization, verifying that coordinate with committor analysis, and measuring the reaction energy profile with umbrella sampling. We also describe our implementation of a termination criterion for aimless shooting based on the Godambe information calculated during model building with likelihood maximization as well as a novel approach to constraining simulations to the desired rare event pathway during umbrella sampling. |
