Code, documentation, experiments we want to retain for reference, but that we're not currently maintaining.

• atom_mapping/ -- distance-based atom comparison for rdFMCS
• autodiff/ -- code related to automatic differentiation
  • surreal.cuh -- implementation of forward-mode AD using complex step differentiation with operator overloading
• docs/ -- write-up of initial vision for timemachine, involving efficient backpropagation through MD trajectories
• docking/ -- Docking module that docks uses non-equilibrium switching
• gpu_tricks/ -- tricks and workarounds for GPU kernel code
• io/ -- Input/output utilities
• jax_tricks -- misc. Jax functions
• modules -- misc. modules
  • reservoir_sampler.py
  • rmsd.py -- compute rmsd under Jax
  • potentials -- deprecated potentials
    • evp.py -- eigenvalue problem solvers for small square matrices
    • pmi.py -- principal moments of inertia related code
    • gbsa.py -- GBSA implicit solvent model
    • shape.py -- Calculate volume overlap between two molecules
  • tests -- deprecated tests
    • test_shape.py -- tests for potentials.shape
    • dual_topology.py -- test with TI and dual topology
• rabfe -- Code previous used in RABFE
  • free_energy.py -- Free Energy classes for RABFE
  • model_rabfe.py -- Models for performing stages of RABFE
  • test_rabfe_topology.py -- Tests for rabfe topologies
  • test_rabfe.py -- Test RABFE
  • topology.py -- RABFE specific topology classes
  • lambda_schedule.py -- Lambda schedules specific to RABFE
  • estimator.py -- Estimating dGs for RABFE
  • restraints.py -- Restraints specific to RABFE
  • test_restraints.py -- Tests for restraints
  • endpoint_correction.py -- Endpoint correction for RABFE
  • test_endpoint_correction.py -- Tests for endpoint correction
• optimize/ -- legacy protocol and forcefield optimization code
• thermo_deriv/ -- numerical experiments with "thermodynamic derivative" estimators, adjusting LJ parameters to match observables
  • note: currently missing dependencies thermo_deriv.lj_non_periodic.lennard_jones, thermo_deriv.lj.lennard_jones.
  • note: langevin_coefficients dependency has since changed -- some scripts rely on a version of langevin_coefficients prior to PR #459
• training/ -- classes and functions for an earlier training workflow
  • note: somewhat tailored to use TI estimates, constant volume simulations, GRPC, ...
• scripts/
  • bootstrap_am1.py -- script for approximating AM1BCC with atom types rather than bond types
  • rhfe_single.py runs three hydration free energy protocols that should give similar results:
    • taking the difference between two absolute hydration free energy calculations (each computed using TI and 4D decoupling)
    • computing a relative free energy using a complete atom-mapping (interpolating the valence energies, and interpolating the nonbonded parameters)
    • computing a relative free energy using a partial atom-mapping (the atom being deleted / inserted is handled using 4D decoupling)
  • rbfe_single.py -- script for running relative binding free energy with single topology
  • estimator_variance.py measures run-to-run variability as a function of number of MD steps performed per run
  • generate_gradients.py use symbolic differentiation for common functional forms to emit CUDA code
  • npt_equilibration.py samples the constant temperature and pressure ensemble for each of several lambda windows, by running thermostatted MD and pausing every few steps to apply a Monte Carlo barostat move
  • ahfe.py runs 4D decoupling simulations of aspirin in a waterbox, for later use in a TI estimator of the absolute hydration free energy.
  • rhfe_dual.py runs 4D decoupling simulations of aspirin and a version of aspirin that mutates an oxygen to a fluorine in a waterbox, subject to a centroid restraint, for later use in a TI estimator of the relative hydration free energy difference between these two compounds.
  • hif2a/ runs calculations on several of the ligands in the hif2a benchmark dataset
    • hif2a/generate_star_map.py generates a "star map" (a single hub and several spokes), and serializes a collection of RelativeFreeEnergy objects for (hub, spoke) pairs
    • hif2a/fit_to_multiple_rbfes.py fits nonbonded parameters to the experimental IC50s associated with these ligands
  • overlap_test.py tests two restraint types, one based on principal moments of inertia and one based on a measure of shape overlap.
  • potential_energy.py computes the potential energy of an "alchemical" system, as well as its derivatives w.r.t. coords, params, or lam
  • run_smc_on_biphenyl.py run smc on a biphenyl test system
  • validate_relative_binding.py run RABFE protocol