README.md

aib9_openmm

Working protocol for setting up solvated Aib9 system using Charmm36m forcefield and running long MD simulation (NPT) in OpenMM.

1. Create a conda environment from the requirements.txt by running the command below

conda create --name aib9 --file requirements.txt -c conda-forge
conda activate aib9

2. Open and run aib9.ipynb using jupyterlab. The following command should open jupyterlab in your browser.

   jupyter lab
   

If you are using this repository for running Aib9 simulations, please cite the following paper:

@article{mehdi2022accelerating,
  title={Accelerating all-atom simulations and gaining mechanistic understanding of biophysical systems through state predictive information bottleneck},
  author={Mehdi, Shams and Wang, Dedi and Pant, Shashank and Tiwary, Pratyush},
  journal={Journal of chemical theory and computation},
  volume={18},
  number={5},
  pages={3231--3238},
  year={2022},
  publisher={ACS Publications}
}