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NIST Disclaimer

Certain commercial equipment, instruments, or materials are identified in this paper to foster understanding. Such identification does not imply recommendation or endorsement by the National Institute of Standards and Technology, nor does it imply that the materials or equipment identified are necessarily the best available for the purpose.

Generate Alchemical LAMMPS Inputs

Functions to generate LAMMPS inputs for alchemical calculations. This package was produced for generating the simulation input file for the completion of the publication "Hydration Contribution to the Solvation Free Energy of Water-Soluble Polymers". These functions include inputs used for thermodynamic integration, Bennett Acceptance Ratio (BAR), or Multi-state Bennett Acceptance Ratio (MBAR).

Documentation

  • locally: Run the following in the command line: python -m generate_alchemical_lammps_inputs -d
  • online: GitHub

Installation

  • Step 1: Download the master branch from our github page as a zip file, or clone it to your working directory with:

    git clone https://github.com/usnistgov/generate_alchemical_lammps_inputs

  • Step 2 (Optional): If you are using conda and you want to create a new environment for this package you may install with:

    conda env create -f generate_alchemical_lammps_inputs/requirements.yaml

  • Step 3: Install package with:

    pip install generate_alchemical_lammps_inputs/.

    or change directories and run

    pip install .

    Adding the flag -e will allow you to make changes that will be functional without reinstallation.

  • Step 4: Initialize pre-commits (for developers)

    pre-commit install

LICENSE

The license in this repository is superseded by the most updated language on of the Public Access to NIST Research Copyright, Fair Use, and Licensing Statement for SRD, Data, and Software.

Contact

Jennifer A. Clark, PhD
Debra J. Audus, PhD (debra.audus@nist.gov)
Jack F. Douglas, PhD

Affiliation

Polymer Analytics Project
Polymer and Complex Fluids Group
Materials Science and Engineering Division
Material Measurement Laboratory
National Institute of Standards and Technology

Citation

Clark, J. A.; Audus, D. J.; Douglas, J. F. Python Package for Generating LAMMPS Input Scripts for Alchemical Processes: Generate_alchemical_lammps_inputs, 2024. https://doi.org/10.18434/mds2-3641.