Molecular simulation · Hard
Hydration free energy by thermodynamic integration
Execute a fixed alchemical protocol across aqueous and gas phases, preserve every AMBER-native artifact, and reconcile per-window evidence with the reported free energy.
Two phases × two interaction legs, each resolved through the same nine declared windows.
Electrostaticvan der WaalsGas phase
9λ windows
9nonlinear windows
Water phase9λ windows
9nonlinear windows
Per-path window schedule
λ start9 fixed pointsλ end
ABCG2 chargesno soft-core potentials
01Prepare systemscharges + topologies
→02Run all windows4 paths × 9 logs
→03Integratecomponent evidence
→04Reconcile handoffJSON + plot + report
9Gaussian-quadrature windows
4phase × interaction paths
2electrostatic and vdW legs
AMBERnative evidence required
Workflow
Prepare the molecule
Apply ABCG2 atomic charges and construct charged-ligand and missing-parameter files.
Build both phases
Create water and gas endpoint topologies, then minimize and equilibrate each system.
Run all windows
Execute electrostatic and nonlinear van der Waals legs at every declared λ value.
Integrate and reconcile
Trace the component and total values back to the per-step DV/DL series in unedited output logs.
Artifact contract
results.jsondvdl_vs_lambda.pngreport.mdcharged ligand + frcmodwater/gas topologiesminimization + equilibration logsall per-window TI outputs