Hamiltonian replica exchange augmented with diffusion-based generative models and importance sampling to assess biomolecular conformational basins and barriers

CLN025.zip Data related to the CLN025 results: REMD/ – Data from REMD simulations traj/300K/ – .gro, .xtc, .top, .mdp files for the replica at 300 K DDPM/ – Training set for DDPM and generated points REST2/ – Data from REST2 simulations traj/300K/ – .gro, .xtc, .top, .mdp files for the reference replica at 300 K DDPM/ – Training set for DDPM and generated points REST2_DES/ – REST2 simulations at 340 K with the CHARMM22* force field (for comparison with the DEShaw trajectory) traj/300K/ – .gro, .xtc, .top, .mdp files for the reference replica at 340 K DDPM/ – Training set for DDPM and generated points PTP1B.zip Data related to the PTP1B results: closed/ – REST2 simulations initiated from the closed conformation traj/300K/ – .gro, .xtc, .top, .mdp, plumed files for the reference replica at 300 K DDPM/ – Training set for DDPM and generated points closed_bias/ – Biased REST2 simulations from the closed conformation traj/300K/ – .gro, .xtc, .top, .mdp, plumed files for the reference replica at 300 K DDPM/ – Training set for DDPM and generated points open/ – Biased REST2 simulations from the open conformation traj/300K/ – .gro, .xtc, .top, .mdp,plumed files for the reference replica at 300 K DDPM/ – Training set for DDPM and generated points