Module: logmfd
| Description | Usage |
|---|---|
| Method for enhanced sampling and for free energy calculations along collective variables | |
| Authors: Tetsuya Morishita, Naoki Watanabe |   |
Details
The LOGMFD module contains the LogMFD/LogPD method for enhanced sampling in a CV space and for on-the-fly free energy reconstruction along the CVs. This module implements the multiple-replica algorithm (see second reference below) as well as the single-replica algorithm (see first reference) the former invoking the Crooks-Jarzynski non-equilibrium work relation. In addition, TAMD/d-AFED, which is discussed in the fourth of the papers cited below, can also be implemented by this module.
Installation
This module is not installed by default. Add --enable-modules=logmfd to your './configure' command when building PLUMED to enable these features.
Actions
The following actions are part of this module
| Name | Description | Tags |
|---|---|---|
| LOGMFD | Used to perform LogMFD, LogPD, and TAMD/d-AFED. | BIAS |
References
More information about this module is available in the following articles:
- T. Morishita, S. G. Itoh, H. Okumura, M. Mikami, Free-energy calculation via mean-force dynamics using a logarithmic energy landscape. Physical Review E. 85 (2012)
- T. Morishita, Y. Yonezawa, A. M. Ito, Free Energy Reconstruction from Logarithmic Mean-Force Dynamics Using Multiple Nonequilibrium Trajectories. Journal of Chemical Theory and Computation. 13, 3106–3119 (2017)
- T. Morishita, T. Nakamura, W. Shinoda, A. M. Ito, Isokinetic approach in logarithmic mean-force dynamics for on-the-fly free energy reconstruction. Chemical Physics Letters. 706, 633–640 (2018)
- J. B. Abrams, M. E. Tuckerman, Efficient and Direct Generation of Multidimensional Free Energy Surfaces via Adiabatic Dynamics without Coordinate Transformations. The Journal of Physical Chemistry B. 112, 15742–15757 (2008)