alchemtest.gmx
The alchemtest.gmx module features datasets generated using the Gromacs molecular dynamics engine. They can be accessed using the following accessor functions:
alchemtest.gmx
load_benzene load_ABFE load_expanded_ensemble_case_1 load_expanded_ensemble_case_2 load_expanded_ensemble_case_3 load_water_particle_with_total_energy load_water_particle_with_potential_energy load_water_particle_without_energy
The data sets contain derivatives of the Hamiltonian (TI) and free energy perturbation (FEP) data suitable for processing with FEP estimators as well as BAR/MBAR. Individual λ windows were run independently.
alchemtest.gmx.load_benzene
Data for extended ensemble simulations; case 1 and case 2 are extended ensembles in the alchemical parameters, case 3 includes replica exchange (REX).
alchemtest.gmx.load_expanded_ensemble_case_1
alchemtest.gmx.load_expanded_ensemble_case_2
alchemtest.gmx.load_expanded_ensemble_case_3
3 simple dH/dl and U_nk datasets of a single water particle from a simulations of water between to hydrophilic surfaces. One dataset contains a total energy column, one contains a potential energy column and one does not contain a energy column.
alchemtest.gmx.load_water_particle_with_total_energy
alchemtest.gmx.load_water_particle_with_potential_energy
alchemtest.gmx.load_water_particle_without_energy
The dataset for computing the absolute binding free energy of n-phenylglycinonitrile to T4 lysozyme. The calculation has two legs: complex and ligand. In the complex leg, restraint is applied to the ligand and the coulombic as well as the Van der Waals interactions are decoupled sequentially. In the ligand leg, only the coulombic and Van der Waals interactions are decoupled.
alchemtest.gmx.load_ABFE