README.md

Permutationally Invariant Networks for Enhanced Sampling (PINES): Discovery of Multi-Molecular and Solvent-Inclusive Collective Variables

Implementation of PINES in PLUMED2

Requirements

• PLUMED2
• MD Engine (GROMACS)

Installation

Case 1: With installed PLUMED2+MD,

• Follow this for reinstalling PLUMED with PINES:
  • Download this repository
  • Execute patch_piv_mesa_plumed.sh <path_to_PLUMED>
  • Re-install PLUMED2 with --enable-modules=all or --enable-modules=pines+annbfunc
• Alternative usage without reinstalling PLUMED:
  • use LOAD command in PLUMED to link in plumed.dat file with the PINES codes in this repository. Example usage can be found in examples/driverTests.

Case 2: New installation of PLUMED2+MD,

• Download this repository
• Download MD Engine & PLUMED2.
• Execute patch_piv_mesa_plumed.sh <path_to_PLUMED>
• Follow standard MD Engine + PLUMED2 installation process with --enable-modules=all or --enable-modules=pines+annbfunc

Examples

• Argon 13 cluster
• C45 in water
• NaCl in water

Parameters

Please refer parameters.md for a template PLUMED file along with annotations explaining each parameter. In case the annotations are not clear, please let us know by opening an issue in this repo.

Citation

If you use this code in your work, please cite:

Herringer, Nicholas SM; Dasetty, Siva; Gandhi, Diya; Lee, Junhee; Ferguson, Andrew L. "Permutationally Invariant Networks for Enhanced Sampling (PINES): Discovery of Multi-Molecular and Solvent-Inclusive Collective Variables." arXiv preprint arXiv:2308.08680. DOI: https://doi.org/10.48550/arXiv.2308.08680

@misc{herringer2023permutationally,
      title={Permutationally Invariant Networks for Enhanced Sampling (PINES): Discovery of Multi-Molecular and Solvent-Inclusive Collective Variables}, 
      author={Nicholas S. M. Herringer and Siva Dasetty and Diya Gandhi and Junhee Lee and Andrew L. Ferguson},
      year={2023},
      eprint={2308.08680},
      archivePrefix={arXiv},
      primaryClass={q-bio.BM}
}