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.