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/ contains Umbrella sampling files

  • umbrella_alad/5_mbar/mbar_analysis.inp MBAR input

• remd_alat/ contains T-REMD files

  • inp MBAR input

• fep_val2trp/ contains FEP files

  • mbar_analysis.inp MBAR input

• grest_alat/ contains gREST files

  • mbar_analysis.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

ymatsunaga@mail.saitama-u.ac.jp