PyGBe Convergence Data: Errors for a Spherical Molecule

Convergence results for PyGBe and APBS solvers using a spherical molecule of radius 4 Armstrong with a centered charge of –1e. Errors were calculated with respect to extrapolated values from Richardson extrapolation. This data supports the 2014 paper 'A biomolecular electrostatics solver using Python, GPUs and boundary elements'.

Use Cases

• Benchmarking solver accuracy based on convergence error data
• Comparing performance between PyGBe and APBS solvers based on the spherical test case
• Validating boundary element method implementations for Poisson-Boltzmann equations
• Assessing GPU-accelerated computational physics code based on the described test results

Strengths

• Errors are calculated with respect to extrapolated values, providing a rigorous benchmark
• Data is directly tied to a published 2014 paper in Computational Physics Communications
• The test case is clearly defined: a spherical molecule of radius 4 Armstrong with a centered charge

Limitations

• Column-level documentation is absent; field semantics must be inferred after download
• Row count is unknown, which may limit suitability assessment
• Last update date is unknown; freshness unverified

Provenance

Source

Christopher D. Cooper, associated with research supported by the Office of Naval Research and NSF.

Collection Method

Generated as part of computational experiments for a published paper.