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Programs and Source Code

Molecular simulation tools

• Perl code for parallel tempering molecular dynamics with AMBER7 [deprecated]
• Weighted histogram analysis method (WHAM) for simulated and parallel tempering
• Automatic state decomposition
• Multistate Bennett acceptance ratio
• Toolkit for aiding in preparing simulations and free energy calculations for gromacs
• Modified gromacs 3.1.4 for expanded ensemble free energy calculations (by Michael Shirts)

Tools for the analysis of experimental data

• Multistate Bennett acceptance ratio for analysis of multiple equilibrium experiments under different bias potentials
• Bayesian analysis of isothermal titration calorimetry (ITC) data