2024-03-29T06:14:09Z
https://nagoya.repo.nii.ac.jp/oai
oai:nagoya.repo.nii.ac.jp:00023838
2023-01-16T04:13:52Z
336:695:696
General Formalism of Mass Scaling Approach for Replica-Exchange Molecular Dynamics and its Application
Nagai, Tetsuro
70696
Replica-exchange molecular dynamics (REMD) has demonstrated its efficiency by combining trajectories of a wide range of temperatures. As an extension of the method, the author formalizes the mass-manipulating replica-exchange molecular dynamics (MMREMD) method that allows for arbitrary mass scaling with respect to temperature and individual particles. The formalism enables the versatile application of mass-scaling approaches to the REMD method. The key change introduced in the novel formalism is the generalized rules for the velocity and momentum scaling after accepted replica-exchange attempts. As an application of this general formalism, the refinement of the viscosity-REMD (V-REMD) method [P. H. Nguyen, J. Chem. Phys. 132, 144109 (2010)] is presented. Numerical results are provided using a pilot system, demonstrating easier and more optimized applicability of the new version of V-REMD as well as the importance of adherence to the generalized velocity scaling rules. With the new formalism, more sound and efficient simulations will be performed.
journal article
日本物理学会
2017-01-15
application/pdf
Journal of the Physical Society of Japan
86
014003
014003
http://dx.doi.org/10.7566/JPSJ.86.014003
http://hdl.handle.net/2237/26004
0031-9015
https://nagoya.repo.nii.ac.jp/record/23838/files/NagaiJPSJ2017.pdf
eng
https://doi.org/10.7566/JPSJ.86.014003
Copyright ©2017 The Physical Society of Japan 日本物理学会