Software & Computational Methods

Methods for following molecular motion.

Computational approaches that connect molecular simulation, enhanced sampling, structural interpretation, and high-performance computing.

01

Molecular simulation

All-atom molecular dynamics and molecular modeling across diverse biomolecular systems.

  • CHARMM
  • AMBER
  • GROMACS
  • NAMD
  • OpenMM
  • AutoDock
  • Schrödinger
02

Enhanced sampling & energetics

Approaches for exploring conformational landscapes, rare events, and molecular energetics beyond routinely accessible timescales.

  • Gaussian accelerated MD
  • Metadynamics
  • Replica exchange MD
  • MM/PBSA
  • Interaction decomposition
03

Trajectory & structural analysis

Analysis workflows that connect molecular ensembles with structural and mechanistic interpretation.

  • MDAnalysis
  • MDTraj
  • cpptraj
  • FreeSASA
  • Clustering
  • Dimensionality reduction
04

Scientific computing

Programming and high-performance computing environments used for simulation, analysis, and method development.

  • Python
  • FORTRAN
  • R
  • Shell
  • Linux
  • HPC / SLURM
  • GPU clusters
  • Anton2
  • Git
05

Methods in development

Ongoing method-development work will be described here after it is ready for public release. No unreleased software is presented as an available tool.

Future releases can add repositories, documentation, examples, and version history without restructuring this page.