diff --git a/src/eds/EDS.cpp b/src/eds/EDS.cpp index 34ff47605cbe0c7196a5897508b19d93b8946f12..d62da5ad3ffa366925c0206d35f99f8e3a7137fb 100644 --- a/src/eds/EDS.cpp +++ b/src/eds/EDS.cpp @@ -36,7 +36,7 @@ using namespace bias; namespace PLMD { namespace eds { -//+PLUMEDOC BIAS EDS +//+PLUMEDOC EDSMOD_BIAS EDS /* Add a linear bias on a set of observables. diff --git a/user-doc/EDSMOD.md b/user-doc/EDSMOD.md new file mode 100644 index 0000000000000000000000000000000000000000..6f02f9180362bf2127ce97b071a4e166aedcc32b --- /dev/null +++ b/user-doc/EDSMOD.md @@ -0,0 +1,30 @@ +\page EDSMOD Experiment Directed Simulation + +<!-- +description: Methods for incorporating additional information about CVs into MD simulations by adaptively determined linear bias parameters +authors: Glen Hocky, Andrew White +reference: \cite white2014efficient \cite hocky2017cgds +--> + +## Overview + +This Experiment Directed Simulation module contains methods for adaptively determining linear bias parameters such that each biased CV samples a new target mean value. This module implements the stochastic gradient descent algorithm in the original EDS paper \cite white2014efficient as well as additional minimization algorithms for Coarse-Grained Directed Simulation \cite hocky2017cgds. + +Notice that a similar method is available as \ref MAXENT, although with different features and using a different optimization algorithm. + +## Installation +This module is not installed by default. Add '\-\-enable-modules=eds' to your './configure' command when building PLUMED to enable these features. + +## Usage +Currently, all features of the EDS module are included in a single EDS bias function: \ref EDS + +A tutorial using EDS specifically for biasing coordination number can be found on <a href="http://thewhitelab.org/Blog/tutorial/2017/05/10/lammps-coordination-number-tutorial/">Andrew White's webpage</a>. + +## Module Contents +- \subpage EDSMODBias + +\page EDSMODBias Biases Documentation + +The following list contains descriptions of biases developed for the PLUMED-EDS module. They can be used in combination with other biases outside of the EDS module. + +@EDSMOD_BIAS@ diff --git a/user-doc/bibliography.bib b/user-doc/bibliography.bib index eda2d69c592f61cbb48ebe227a655e426b5d2cfc..08a73058fa627e964a7da7361360c444aba6f0d4 100644 --- a/user-doc/bibliography.bib +++ b/user-doc/bibliography.bib @@ -2439,6 +2439,17 @@ volume = {10}, year = {2014} } +@article{hocky2017cgds, +author = {Hocky, Glen M. and Dannenhoffer-Lafage, Thomas and Voth, Gregory A.}, +title = {Coarse-Grained Directed Simulation}, +journal = {Journal of Chemical Theory and Computation}, +volume = {13}, +number = {9}, +pages = {4593-4603}, +year = {2017}, +doi = {10.1021/acs.jctc.7b00690}, +} + @article{cunha2017unraveling, title={Unraveling Mg2+--RNA binding with atomistic molecular dynamics}, author={Cunha, Richard A and Bussi, Giovanni},