Collaborate to decorrelate in path space: Hamiltonian replica exchange transition interface sampling (HRETIS)

The files provided here contain examples of 1D, 2D, and coarse-grained systems that demonstrate Hamiltonian exchange within the Hamiltonian Replica Exchange Transition Interface Sampling (HRETIS) framework. The coarse-grained (MARTINI 3) path sampling simulations show the permeation of glutamine (P2-P5) and methionine (P2-C6) through a DPPC membrane at 323 K using GROMACS. These simulations can be resumed from the existing "restart.toml" files located in the following directories:CG/path_sampling_set_2/RETIS_main_1/infretis/CG/path_sampling_set_2/HRETIS_75_1/infretis/CG/path_sampling_set_2/RETIS_helper_1/infretis/The command to continue a run using the infretis package (https://github.com/infretis/infretis) is:infretisrun -i restart.tomlThe simulations can also be started from scratch by copying the initial paths from:CG/path_sampling_set_2/initial_paths/into the "infretis/load" directory of each simulation. After that, the run can be started with:infretisrun -i infretis.tomlAdditional information about running the 1D and 2D simulations, the directory structure, and the simulation input files is provided in the "readme.txt" file.