TSMD
Python implementations of TS-MD* and PaCS-MD**. Our implementations use GROMACS command for all of the manipulation about MD simulation. The required version is GROMACS 2016.5.
* K. Shin, D. P. Tran, K. Takemura, A. Kitao, K. Terayama, and K. Tsuda, “Enhancing biomolecular sampling with reinforcement learning: tree search molecular dynamics simulation method,” ACS Omega, 2019. [DOI: 10.1021/acsomega.9b01480]
** R. Harada and A. Kitao, “Parallel cascade selection molecular dynamics (PaCS-MD) to generate conformational transition pathway,” J. Chem. Phys., 139, 07B611 1. (2013)
Kento Shin
Master
Publications
Enhancing Biomolecular Sampling with Reinforcement Learning: A Tree Search Molecular Dynamics Simulation Method
This paper proposes a novel molecular simulation method, called tree search molecular dynamics (TS-MD), to accelerate the sampling of …