diff --git a/timemachine/fe/rbfe.py b/timemachine/fe/rbfe.py index 4b6d34873..cbc891891 100644 --- a/timemachine/fe/rbfe.py +++ b/timemachine/fe/rbfe.py @@ -752,6 +752,7 @@ def estimate_relative_free_energy_bisection_hrex( n_windows: Optional[int] = None, min_overlap: Optional[float] = None, min_cutoff: Optional[float] = 0.7, + use_smoothcore: Optional[bool] = False, ) -> HREXSimulationResult: """ Estimate relative free energy between mol_a and mol_b using Hamiltonian Replica EXchange (HREX) sampling of a diff --git a/timemachine/potentials/nonbonded.py b/timemachine/potentials/nonbonded.py index 58363870f..5f76be609 100644 --- a/timemachine/potentials/nonbonded.py +++ b/timemachine/potentials/nonbonded.py @@ -970,8 +970,8 @@ def smoothcore_lj_interpolation(lamb, lj_src, lj_dst, mol_a_idxs, mol_b_idxs): lj_dst_stable[mol_b_idxs] = lj_dst[mol_b_idxs] lj_interpolated = np.repeat([MIN_SIG_EPS], len(lj_src), axis=0) - lj_interpolated[mol_a_idxs] += np.clip((1 - lamb) * 10, 0, 1) * lj_src[mol_a_idxs] - lj_interpolated[mol_b_idxs] += np.clip(lamb * 10, 0, 1) * lj_dst[mol_b_idxs] + lj_interpolated[mol_a_idxs] += np.clip((1 - lamb) * 5, 0, 1) * lj_src[mol_a_idxs] + lj_interpolated[mol_b_idxs] += np.clip(lamb * 5, 0, 1) * lj_dst[mol_b_idxs] return lj_interpolated