ScMile: A Script to Investigate Kinetics with Short Time Molecular Dynamics Trajectories and the Milestoning Theory

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.