This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration free energies or ligand binding free energies.
Adding the improvements of the OpenMM implementation to the main branch. The idea is to include the previously carried out work on the OpenMM implementation in the main project, while development of the OpenMM/RE-EDS pipeline continues in another branch.
Changes compared to the previous RE-EDS OpenMM version
Parallel implementation on multiple GPUs with OpenMPI (used by default in the examples/openmm/ scripts).
Parallel implementation + openmm.CustomIntegrator, does EDS simulations with a LangevinMiddleIntegrator which scales the forces in the GPU at each step. Since only forces of the end-states are scaled and not the energies, the MonteCarloBarostat works incorrectly and possibly yields unphysical results.
Parallel implementation + openmm.CustomCVForce, correctly scales the energies at each step but is also much slower.
Added example scripts to apply the RE-EDS pipeline on solvation free energies of a set of small molecules, and binding free energies for CHK1 ligands.
Description
Adding the improvements of the OpenMM implementation to the main branch. The idea is to include the previously carried out work on the OpenMM implementation in the main project, while development of the OpenMM/RE-EDS pipeline continues in another branch.
Changes compared to the previous RE-EDS OpenMM version
openmm.CustomIntegrator, does EDS simulations with aLangevinMiddleIntegratorwhich scales the forces in the GPU at each step. Since only forces of the end-states are scaled and not the energies, the MonteCarloBarostat works incorrectly and possibly yields unphysical results.openmm.CustomCVForce, correctly scales the energies at each step but is also much slower.Status