Post String Method

The post sting method estimates the minimal free energy path on the free energy landscape.

DEMO

Demonstration for the open-closed transition of ribose binding protein.

Features

The replacement of the nth beads.

Requirement (validated version)

• Python 3.x (3.7.8)
• matplotlib (3.3.1)
• pyEMMA (2.5.7)
• numpy (1.19.1)
• tqdm (4.48.2)

Installation

Launch string.ipynb and load post-string-input.xvg. post-string-input.xvg should contain three column data (x, y, weight).

Usage

Note

Please cite this paper.

Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada. A post-process to estimate an approximated minimal free energy path based on local centroids. Chem. Phys. Lett. (2021)DOI:[https://doi.org/10.1016/j.cplett.2021.139003]

Author

• Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada.
• Center for Computational Sciences, University of Tsukuba
• morita@ccs.tsukuba.ac.jp

License

Post string method is under MIT license.