physical validation

physical validation detects unphysical behavior in molecular dynamics (MD) and Monte Carlo (MC) simulations to assess and improve the physical correctness of simulation setups and simulation software for systems such as proteins, membranes, DNA, lipid bilayers, peptides, polymers, and liquid properties.

Key Features:

• User-implemented tests: Provides tests users can run on MD programs, ranging from post-processing analyses to additional simulations, to evaluate physical correctness of setups.
• Error detection: Identifies non-conservative integrators, deviations from the Boltzmann ensemble, and lack of ergodicity between degrees of freedom.
• Code correctness testing: Integrates physical validation tests into code-checking mechanisms so simulation software releases undergo physical sanity checks on representative systems.
• System coverage: Targets systems including proteins, DNA, membranes, lipid bilayers, peptide dynamics, polymer behaviors, and liquid properties.
• GROMACS integration: Incorporated into the GROMACS release process to require physical sanity checks for major releases.

Scientific Applications:

• Simulation validation: Improves reliability and robustness of MD and MC simulations used to predict experimental observables for proteins, membranes, and polymeric materials.
• Diagnosis of simulation artifacts: Detects and diagnoses simulation setup and software errors that can affect protein and DNA folding, lipid bilayer properties, peptide dynamics, polymer behaviors, and liquid properties.
• Software quality assurance: Serves as a pre-release quality control mechanism for molecular mechanics software through physical sanity checks (e.g., GROMACS).

Methodology:

Employs a two-fold approach of user-implemented tests (post-processing analyses to additional simulations) and integration of physical validation tests into software code-checking mechanisms to run sanity checks on representative systems.