Software
Software tools used in molecular simulation, quantum chemistry, visualization, and analysis.
A visual toolkit for computational science.
Rather than presenting software as a long list, this page groups the lab’s tools by the role they play in a computational workflow — simulation, quantum chemistry, visualization, and analysis.
Molecular Simulation
Core engines for biomolecular dynamics, force-field testing, and large-scale simulations.
AMBER
A widely used suite for biomolecular simulation and force-field development.
Visit resource ↗CHARMM
Molecular mechanics and dynamics software for biomolecular systems.
Visit resource ↗NAMD
Highly scalable molecular dynamics for large biomolecular systems.
Visit resource ↗GROMOS
Molecular simulation software and force-field ecosystem.
Visit resource ↗GROMACS
Fast, open-source molecular dynamics and analysis platform.
Visit resource ↗Quantum Chemistry
Electronic-structure tools for energies, geometries, and molecular properties.
Gaussian
Electronic-structure calculations for molecular systems.
Visit resource ↗GAMESS
General ab initio molecular electronic structure system.
Visit resource ↗Q-Chem
Quantum chemistry software for electronic-structure modeling.
Visit resource ↗NWChem
Open-source computational chemistry for molecular and condensed systems.
Visit resource ↗Visualization & Analysis
Tools used to inspect structures, prepare molecules, analyze trajectories, and work with experimental data.
VMD
Interactive molecular visualization and trajectory analysis.
Visit resource ↗Open Babel
Chemical file conversion and cheminformatics utilities.
Visit resource ↗3DNA
Structural analysis, rebuilding, and visualization of nucleic acids.
Visit resource ↗UCSF Sparky
NMR assignment and analysis environment.
Visit resource ↗NMRPipe
Processing and analysis tools for multidimensional NMR data.
Visit resource ↗GNUPlot
Flexible scientific plotting and data visualization.
Visit resource ↗