ArticleJournal of chemical theory and computation2020
ScMile: A Script to Investigate Kinetics with Short Time Molecular Dynamics Trajectories and the Milestoning Theory.
Article in Journal of chemical theory and computation, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
What it found
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Who cites it
4 citing papers in PubMed.
- Exploring Biomolecular Conformational Dynamics with Polarizable Force Field AMOEBA and Enhanced Sampling Method Milestoning.Journal of chemical theory and computation · 2024Article
- ScMiles2: A Script to Conduct and Analyze Milestoning Trajectories for Long Time Dynamics.Journal of chemical theory and computation · 2022Article
- WESTPA 2.0: High-Performance Upgrades for Weighted Ensemble Simulations and Analysis of Longer-Timescale Applications.Journal of chemical theory and computation · 2022Article
- Side-Chain Polarity Modulates the Intrinsic Conformational Landscape of Model Dipeptides.The journal of physical chemistry. B · 2021Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Studies of complex and rare events in condensed phase systems continue to attract considerable attention. Milestoning is a useful theory and algorithm to investigate the long-time dynamics of activated molecular events. It is based on launching a large number of short trajectories and statistical analysis of the outcome. The implementation of the theory in a computer script is described that enables more efficient Milestoning calculation, reducing user time and errors, and automating a significant fraction of the algorithm. The script exploits a molecular dynamics engine, which at present is NAMD, to run the short trajectories. However, since the script is external to the engine, the script can be easily adapted to different molecular dynamics codes. The outcomes of the short trajectories are analyzed to obtain a kinetic and thermodynamic description of the entire process. While many examples of Milestoning were published in the past, we provide two simple examples (a conformational transition of alanine dipeptide in a vacuum and aqueous solution) to illustrate the use of the script.
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Registered trials
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