From d6dd93d29e987eed1d3507c43d8feafad2a1fb17 Mon Sep 17 00:00:00 2001
From: Giovanni Bussi <giovanni.bussi@gmail.com>
Date: Mon, 29 Jul 2013 08:55:14 +0200
Subject: [PATCH] Several fixes in references
---
src/bias/MetaD.cpp | 2 ++
src/bias/MovingRestraint.cpp | 6 ++++--
src/colvar/Energy.cpp | 4 +++-
src/multicolvar/DHEnergy.cpp | 2 +-
user-doc/bibliography.bib | 11 +++++++++++
5 files changed, 21 insertions(+), 4 deletions(-)
diff --git a/src/bias/MetaD.cpp b/src/bias/MetaD.cpp
index 01ae2c74a..490bb506a 100644
--- a/src/bias/MetaD.cpp
+++ b/src/bias/MetaD.cpp
@@ -487,6 +487,8 @@ isFirstStep(true)
"Barducci, Bussi, and Parrinello, Phys. Rev. Lett. 100, 020603 (2008)");
if(mw_n_>1) log<<plumed.cite(
"Raiteri, Laio, Gervasio, Micheletti, Parrinello, J. Phys. Chem. B 110, 3533 (2006)");
+ if(adaptive_!=FlexibleBin::none) log<<plumed.cite(
+ "Branduardi, Bussi, and Parrinello, J. Chem. Theory Comput. 8, 2247 (2012)");
log<<"\n";
diff --git a/src/bias/MovingRestraint.cpp b/src/bias/MovingRestraint.cpp
index 5bca9c623..2ab5d3fde 100644
--- a/src/bias/MovingRestraint.cpp
+++ b/src/bias/MovingRestraint.cpp
@@ -31,8 +31,10 @@ namespace bias{
//+PLUMEDOC BIAS MOVINGRESTRAINT
/*
-Add a time-dependent, harmonic restraint on one or more variables, this form
-of bias can be used to performed steered MD and Jarzynski sampling \cite jarzynski.
+Add a time-dependent, harmonic restraint on one or more variables.
+
+This form of bias can be used to performed steered MD \cite Grubmuller3
+and Jarzynski sampling \cite jarzynski.
The harmoic restraint on your system is given by:
diff --git a/src/colvar/Energy.cpp b/src/colvar/Energy.cpp
index 144dc3baf..c2c404909 100644
--- a/src/colvar/Energy.cpp
+++ b/src/colvar/Energy.cpp
@@ -34,6 +34,8 @@ namespace colvar{
/*
Calculate the total energy of the simulation box.
+Total energy can be biased with umbrella sampling \cite bart-karp98jpcb or with well tempered metadynamics \cite Bonomi:2009p17935.
+
\par Examples
The following input instructs plumed to print the energy of the system
\verbatim
@@ -74,7 +76,7 @@ PLUMED_COLVAR_INIT(ao)
getPntrToValue()->resizeDerivatives(1);
log<<" Bibliography ";
log<<plumed.cite("Bartels and Karplus, J. Phys. Chem. B 102, 865 (1998)");
- log<<plumed.cite("Bonomi, Barducci, and Parrinello, J. Comp. Chem. 30, 1615 (2009)");
+ log<<plumed.cite("Bonomi and Parrinello, J. Comp. Chem. 30, 1615 (2009)");
log<<"\n";
}
diff --git a/src/multicolvar/DHEnergy.cpp b/src/multicolvar/DHEnergy.cpp
index d63948386..7a27f8d89 100644
--- a/src/multicolvar/DHEnergy.cpp
+++ b/src/multicolvar/DHEnergy.cpp
@@ -80,7 +80,7 @@ df(2)
std::string DHEnergy::function_description(){
std::ostringstream ostr;
- ostr<<"the Debye-Huckel interaction energy "<<getAction()->plumed.cite("Do, Carloni, Varani and Bussi, submitted (2013)")<<".";
+ ostr<<"the Debye-Huckel interaction energy "<<getAction()->plumed.cite("Do, Carloni, Varani and Bussi, J. Chem. Theory Comput. 9, 1720 (2013)")<<".";
ostr<<" Parameters : temperature "<<T<<" K, ionic strength "<<I<<" M, ";
ostr<<"solvent dielectric constant "<<epsilon;
return ostr.str();
diff --git a/user-doc/bibliography.bib b/user-doc/bibliography.bib
index f970c08cd..9361f6cac 100644
--- a/user-doc/bibliography.bib
+++ b/user-doc/bibliography.bib
@@ -1936,3 +1936,14 @@ volume = {117},
number = {6},
pages = {1838--1843},
}
+
+@article{bart-karp98jpcb,
+ title={{Probability Distributions for Complex Systems: Adaptive Umbrella Sampling of the Potential Energy}},
+ author={Bartels, C. and Karplus, M.},
+ journal={J.~Phys.~Chem.~B},
+ volume={102},
+ number={5},
+ pages={865--880},
+ year={1998},
+ publisher={ACS Publications}
+}
--
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