@article{81571cbb331a451bba9c547f50aceb55,
title = "Isokinetic approach in logarithmic mean-force dynamics for on-the-fly free energy reconstruction",
abstract = "Logarithmic mean-force dynamics (LogMFD) is one of free energy calculation methods that utilize fictitious dynamical variables for efficient conformational sampling. In this study, we extend the LogMFD method to incorporate the isokinetic dynamics for the fictitious dynamical variables. The isokinetic LogMFD approach requires no additional parameter for thermostatting and it obviates the issue associated with the dynamics of the thermostat variable in Nos{\'e}-Hoover type thermostats. These virtues therefore make it easier to set up and undertake LogMFD calculations. The validity of the isokinetic algorithm introduced in LogMFD is examined by a benchmark system of alanine dipeptide in explicit water.",
keywords = "Free energy, Isokinetic dynamics, Logarithmic mean-force dynamics, Molecular dynamics, Protein conformational change, Protein structure, Thermostat",
author = "Tetsuya Morishita and Takenobu Nakamura and Wataru Shinoda and Ito, {Atsushi M.}",
note = "Funding Information: This work was supported in part by a Grant-in-Aid for Scientific Research from JSPS KAKENHI (grant number: 17K05620 ), and by New Energy and Industrial Technology Development Organization of Japan (NEDO) Grant ( P16010 ). The computations were performed on the computational facilities at the Research Institute for Information Technology, Kyushu University, and at the Research Center for Computational Science, NINS, Japan. Publisher Copyright: {\textcopyright} 2018",
year = "2018",
month = aug,
day = "16",
doi = "10.1016/j.cplett.2018.07.011",
language = "English",
volume = "706",
pages = "633--640",
journal = "Chemical Physics Letters",
issn = "0009-2614",
publisher = "Elsevier",
}