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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

John Hymel's Projects

2d-ising-model icon 2d-ising-model

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

calixarenexyz icon calixarenexyz

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.

fixed_voltage_redox_openmm icon fixed_voltage_redox_openmm

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

jhymel icon jhymel

Personal repository associated with Github profile banner.

mm_base icon mm_base

parent MM classes to be imported as submodule

molssi-workshop icon molssi-workshop

Work from the Molecular Sciences Institute's (MolSSI) workshop at the 2019 Southeastern Theoretical Chemistry Association (SETCA) meeting.

nwchem_scripts icon nwchem_scripts

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-beam Theory Group at the Nanomaterials Theory Institute during ORNL-HERE Internship (Spring 2020).

openmm icon openmm

OpenMM is a toolkit for molecular simulation using high performance GPU code.

openmm_qm_mm icon openmm_qm_mm

Hacked verison of OpenMM designed for running the McDaniel lab's QM/MM/PME code

psi4 icon psi4

Open-Source Quantum Chemistry – an electronic structure package in C++ driven by Python

wham icon wham

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

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