FBMS-Lab Softwares

Morphing method for Obtaining Visualized Essential dynamics using DNN and MD Simulations (MOVE DM)
(The link is currently under construction. MOVE-DM is scheduled to be made available online after the publication of the paper.)

MOVE DM is a morphing program that integrates DNN and MD simulations. This tool allows users to visually demonstrate the essential dynamics of any given process. To utilize MOVE DM, only the trajectories of a protein and three physical variable trajectories are required. For systems with two states, MD simulations should be conducted in each state separately. Subsequently, the trajectories of both states are combined into a single trajectory.

• MOVE DM: Morphing method for obtaining visualized essential dynamics using DNN and MD simulations, Naoyuki Miyashita*, Ryota Kiyooka, Shota Simogochi, to be submitted. (2023)

Replica-Exchange INterface ( REIN )  (2011)

    Rein serves as the interface for a replica-exchange simulation. Currently, it supports NAMD as the molecular dynamics (MD) engine for replica-exchange molecular dynamics simulations. However, with modifications, Rein can be adapted to work with any MD software. It was originally developed for the K-computer. (GPL 3.0)

• REIN: Replica-Exchange INterface for Simulating Protein Dynamics and Function, Naoyuki Miyashita, Suyon Re, Yugi Sugita*, International Journal of Quantum Chemistry 115(5) 325-332, Mar. 2015