Implementations of replica-permutation and replica sub-permutation methods into LAMMPS
The replica-permutation method (RPM) and the replica sub-permutation method (RSPM) have been proposed as improved alternatives to the replica-exchange method (REM). Here, we implemented the RPM and RSPM in the NVT and NPT ensembles into an open-source classical molecular dynamics package, LAMMPS. We applied the RPM and RSPM to a polyethylene chain in vacuum and an alanine dipeptide in explicit water to test the implemented codes. We demonstrated that the RPM and RSPM by our codes achieved higher transition ratios of temperatures and faster convergence of physical quantities than the REM. We also validated that the RPM and RSPM generate statistical ensembles correctly.