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Implementation of PINES in PLUMED2

• PLUMED2
• MD Engine (GROMACS)

Case 1: With installed PLUMED2+MD,

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

Case 2: New installation of PLUMED2+MD,

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

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

Please referparameters.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.

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}}