8000 jhymel (John Hymel) · GitHub
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Achievements

Achievement: Pull SharkAchievement: Arctic Code Vault Contributor

Achievements

Achievement: Pull SharkAchievement: Arctic Code Vault Contributor

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jhymel/README.md

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Current project(s)

  • MM_base: Libraries for running basic molecular dynamics (MD) simulations in OpenMM
  • Fixed_Voltage_OpenMM: Libraries for simulating an electrode/electrolyte interface under applied voltage
  • QM/MM/MD: Libraries for fantastic QM/MM dynamics code written by John Pederson using Psi4 and OpenMM
  • WHAM: Implementations of the Weighted Histogram Analysis Method (WHAM) in 1D and 2D
  • Well-sliced Metadynamics Reweighting: Code for reweighting biased simulations incorporating combined metadynamics and umbrella sampling

Pinned Loading

  1. WHAM WHAM Public

    Implementation of the Weighted Histogram Analysis Method (WHAM) in 1D and 2D written in Python

    Python 5

  2. Well-sliced-metadynamics-reweighting Well-sliced-metadynamics-reweighting Public

    Implementation of well-sliced metadynamics reweighting in Python

    Python 1

  3. Fixed_Voltage_Redox_OpenMM Fixed_Voltage_Redox_OpenMM Public

    Scripts, libraries, and forcefield files for running fixed-voltage molecular dynamics simulations using OpenMM. Added functionality for computing free energies for oxidation-reduction reactions.

    Python

  4. 2D-Ising-Model 2D-Ising-Model Public

    2D Ising model project, created as part of statistical mechanics course (Chem 6481) during Fall 2020.

    Jupyter Notebook

  5. NWChem_Scripts NWChem_Scripts Public

    Scripts built for preparing and running NWChem calculations. Primary focus is on setting up multiple QMD/AIMD simulations, each with different starting parameters. Developed while working with E-be…

    Python

  6. CalixareneXYZ CalixareneXYZ Public

    Database of functionalized calixarenes interacting with CO2. All structures created using a MD confirmational search piped into DFT optimization at the PBE-D3(BJ)/def2-TZVP level of theory.

    1

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