Implementations of replica-permutation and replica sub-permutation methods into LAMMPS

M Yamauchi and G La Penna and SG Itoh and H Okumura, COMPUTER PHYSICS COMMUNICATIONS, 276, 108362 (2022).

DOI: 10.1016/j.cpc.2022.108362

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 NV T 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. Program summaryProgram Title: temper/permutation, temper/subpermutation, temper/permutation/npt, and temper/subpermutation/npt CPC Library link to program files: https://doi .org /10 .17632 /t8pbjy8zb7.1 Developer's repository link: https://github .com /MasatakaYm /lammps -rpm-rspm Licensing provisions: GNU General Public License, version 3 Programming language: C++/MPI Nature of problem: The replica-permutation and replica sub-permutation methods 1-3 require implementations to construct permutation or sub-permutation function, to divide replicas into subsets when many replicas are used, and to attempt permutation by the Suwa-Todo algorithm 4. Solution method: We have implemented the replica- permutation and replica sub-permutation methods as an extension of existing temper command of LAMMPS. References1 S.G. Itoh, H. Okumura, J. Chem. Theory Comput. 9 (2013) 570. 2 M. Yamauchi, H. Okumura, J. Chem. Phys. 147 (2017) 184107. 3 M. Yamauchi, H. Okumura, J. Comput. Chem. 40 (2019) 2694. 4 H. Suwa, S. Todo, Phys. Rev. Lett. 105 (2010) 120603. (c) 2022 Elsevier B.V. All rights reserved.

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