Tetsuya Morishita*, Takenobu Nakamura, Wataru Shinoda, Atsushi M. Ito
Chem. Phys. Lett. 706, 633-640 (2018).
Logarithmic mean-force dynamics (LogMFD) is one of free energy calculation methods that utilize ficti- tious 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 associ- ated with the dynamics of the thermostat variable in Nosé-Hoover type thermostats. These virtues there- fore 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.