vtlim / plot_potential

Plot individual potential functions that comprise force fields. Ideal for presentations. Includes energy terms for bonds (harmonic), angles (harmonic), proper torsion (periodic cosine), improper torsion (harmonic), van der Waals (Lennard-Jones), electrostatics (Coulomb), and the Morse potential.

👋 Hi! I'm Victoria

I write docs. Past identities include computational chemistry researcher and patent scientist. My GitHub repos mostly pertain to one of those three categories—tech writing, science, or patents.

📝 Technical writing

• tech-docs: Jupyter notebooks for technical exploration (e.g., Kafka + Druid); scripts for docs infrastructure

🔬 Science

• plot_potential: visualize functions that comprise molecular mechanics force fields (figures for presentations)
• misc: basic stats and plots (figures for publications); configuration for Grace and VMD; OpenEye OEChem utilities
• dihedral-scan: determine the potential energy function of a dihedral angle in a molecule using NAMD
• benchmarkff: comparison of optimized geometries and energies from various force fields with respect to a QM reference
• off_psi4: quantum mechanical analysis of molecular conformers (moved to MobleyLab/quanformer)
• permeability: data analysis from NAMD simulations on calculating membrane permeabilities
• GLIC: analysis and visualization for cryo-EM density-fitting simluations using GROMACS
• Hv1: setup and analysis of free energy perturbation calculations of the Hv1 protein using NAMD
• mismatch: web app to find mismatched base pairs between hybridized DNA sequences

🌎 Patents

• patfam: web app for analysis of patent families across different jurisdictions (collaborations welcome! 👯)
• textsmoosh: web app to process and combine multi-line text into a single line
• excel: (private) scripts for Microsoft Excel to automate processing in vitro and in vivo hit-to-lead results from thousands of HTS biomolecules