https://github.com/matsunagalab/paper_mbar

Input files used in the paper on MBAR by Matsunaga et al.
https://github.com/matsunagalab/paper_mbar

molecular-dynamics multistate-bennett-acceptance-ratio

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Input files used in the paper on MBAR by Matsunaga et al.

• Host: GitHub
• URL: https://github.com/matsunagalab/paper_mbar
• Owner: matsunagalab
• License: gpl-3.0
• Created: 2022-08-31T08:47:19.000Z (over 2 years ago)
• Default Branch: main
• Last Pushed: 2022-10-18T08:37:36.000Z (over 2 years ago)
• Last Synced: 2024-11-19T00:46:19.525Z (2 months ago)
• Topics: molecular-dynamics, multistate-bennett-acceptance-ratio
• Language: Rich Text Format
• Homepage:
• Size: 83.9 MB
• Stars: 0
• Watchers: 2
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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# MBAR input files used in Matsunaga et al.

This repository contains input files for MBAR calculations used in "Use of multistate Bennett acceptance ratio method for free-energy calculations from enhanced sampling and free energy perturbation" by Matsunaga et al.

The files covers all the MBAR calculations except for the QM/MM case, the files of which are available from the authors upon reasonable request. 

All of the input files for mbar_analysis tool provided with the molecular dynamcis simulation software GENESIS.

## Descriptions on files

The files are organied as follows:

- [umbrella_alad/](https://github.com/matsunagalab/paper_mbar/tree/main/umbrella_alad) contains Umbrella sampling files

  - [umbrella_alad/5_mbar/mbar_analysis.inp](https://github.com/matsunagalab/paper_mbar/blob/main/umbrella_alad/5_mbar/mbar_analysis.inp) MBAR input

- [remd_alat/](https://github.com/matsunagalab/paper_mbar/tree/main/remd_alat) contains T-REMD files

  - [inp](https://github.com/matsunagalab/paper_mbar/blob/main/remd_alat/5_analysis/mbar/inp) MBAR input

- [fep_val2trp/](https://github.com/matsunagalab/paper_mbar/tree/main/fep_val2trp) contains FEP files

  - [mbar_analysis.inp](https://github.com/matsunagalab/paper_mbar/blob/main/fep_val2trp/5_analysis/mbar_analysis.inp) MBAR input

- [grest_alat/](https://github.com/matsunagalab/paper_mbar/tree/main/grest_alat) contains gREST files

  - [mbar_analysis.inp](https://github.com/matsunagalab/paper_mbar/blob/main/grest_alat/5_analysis/5-4_mbar/mbar/mbar.inp) MBAR input

## Acknowledgement

We thank the authors of GENESIS tutorials https://www.r-ccs.riken.jp/labs/cbrt/tutorials2022/ . Some of the input files are based on the tutorial files. 

## License

This repository is licensed under the under the terms of GNU General Public License v3.0 (except for the files taken from GENESIS tutorials).

 

## Contact

Yasuhiro Matsunaga

[email protected]