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dock-postprocess v0.2.0
This release adds explicit-solvent molecular dynamics support and expands force-field configuration throughout the OpenMM workflow.
Highlights
- Added
dock-mdfor molecular dynamics with OpenMM - NVT and NPT ensembles supported
- Controlled heating, equilibration, and production stages
- Explicit-solvent support with PME
- Vacuum (no-solvent) mode retained
- Configurable protein, ligand, and water force fields
- Protein support for ff14SB, ff19SB, and ff15ipq
- Ligand support for installed OpenFF and GAFF force fields
- Water models including TIP3P, TIP3P-FB, TIP4P-Ew, TIP4P-FB, SPC/E, OPC, and OPC3
- Configurable ionic strength, solvent padding, box shape, and nonbonded cutoff
- CUDA platform support
- MD trajectories, state reporting, checkpoints, final structures, and metadata
- Preserved support for receptor-specific residue variants and metal coordination restraints
Validation
See VALIDATION_0.2.0.md for validation details.