Module: drr
| Description | Usage |
|---|---|
| an implementation of the extended-system adaptive biasing force (eABF) method | |
| Authors: Haochuan Chen and Haohao Fu |   |
Details
Overview
This module contains the eABF/DRR method to do free energy calculation or enhance sampling along CVs.
Installation
This module is not installed by default and depends on the boost serialization module. Please make sure the boost serialization library is compiled and installed in your system before trying to compile this module. Add '--enable-modules=drr --enable-boost_serialization' to your './configure' command when building PLUMED to enable these features.
Usage
Please read the documentation for the actions and command line tools detailed below.
Actions
The following actions are part of this module
| Name | Description | Tags |
|---|---|---|
| DRR | Used to performed extended-system adaptive biasing force (eABF) | EABFMOD_BIAS |
Command line tools
The following command line tools are part of this module
| Name | Description |
|---|---|
| drr_tool | Extract or merge the drrstate files. |
References
More information about this module is available in the following articles:
- T. Lelièvre, M. Rousset, G. Stoltz, Computation of free energy profiles with parallel adaptive dynamics. The Journal of Chemical Physics. 126 (2007)
- L. Zheng, W. Yang, Practically Efficient and Robust Free Energy Calculations: Double-Integration Orthogonal Space Tempering. Journal of Chemical Theory and Computation. 8, 810–823 (2012)
- H. Chen, H. Fu, X. Shao, C. Chipot, W. Cai, ELF: An Extended-Lagrangian Free Energy Calculation Module for Multiple Molecular Dynamics Engines. Journal of Chemical Information and Modeling. 58, 1315–1318 (2018)
- A. Lesage, T. Lelièvre, G. Stoltz, J. Hénin, Smoothed Biasing Forces Yield Unbiased Free Energies with the Extended-System Adaptive Biasing Force Method. The Journal of Physical Chemistry B. 121, 3676–3685 (2016)
- H. Fu, X. Shao, C. Chipot, W. Cai, Extended Adaptive Biasing Force Algorithm. An On-the-Fly Implementation for Accurate Free-Energy Calculations. Journal of Chemical Theory and Computation. 12, 3506–3513 (2016)
- T. Zhao, H. Fu, T. Lelièvre, X. Shao, C. Chipot, W. Cai, The Extended Generalized Adaptive Biasing Force Algorithm for Multidimensional Free-Energy Calculations. Journal of Chemical Theory and Computation. 13, 1566–1576 (2017)