PaCS-Toolkit

Overview

PaCS-Toolkit is an optimized software utility enabling the use of different MD software and trajectory analysis tools to facilitate the execution of the PaCS-MD simulation and analyze the obtained trajectories, including the preparation for the subsequent construction of the Markov state model. It is coded with Python, is compatible with various computing environments, and allows for easy customization by editing the configuration file and specifying the MD software and analysis tools to be used.

Document

Available from here

Code

Available from here

Examples

Available from here

Reference

"PaCS-Toolkit: Optimized Software Utilities for Parallel Cascade Selection Molecular Dynamics (PaCS-MD) Simulations and Subsequent Analyses"
Shinji Ikizawa, Tatsuki Hori, Tegar Nurwahyu Wijaya, Hiroshi Kono, Zhen Bai, Tatsuhiro Kimizono, Wenbo Lu, Duy Phuoc Tran, and Akio Kitao
J Phys Chem B, 128, 3631 (2024).