From ab475390219a692e59e84b82309172afa6cd95aa Mon Sep 17 00:00:00 2001
From: Giovanni Bussi <giovanni.bussi@gmail.com>
Date: Tue, 3 May 2016 19:23:20 +0200
Subject: [PATCH] Draft manual for target and dampfactor

---
 src/bias/MetaD.cpp        | 29 ++++++++++++++++++++++++++
 user-doc/bibliography.bib | 43 +++++++++++++++++++++++++++++++++++++++
 2 files changed, 72 insertions(+)

diff --git a/src/bias/MetaD.cpp b/src/bias/MetaD.cpp
index 12c94a232..f194cc2b7 100644
--- a/src/bias/MetaD.cpp
+++ b/src/bias/MetaD.cpp
@@ -260,6 +260,30 @@ factor that can then be used to determine the rate. This method can be used toge
 with \ref COMMITTOR analysis to stop the simulation when the system get to the target basin.
 It must be used together with Well-Tempered Metadynamics.
 
+\par
+You can also provide a target distribution using the keyword TARGET
+\cite white2015designing
+\cite marinelli2015ensemble
+\cite gil2016empirical
+The TARGET should be a grid containing a free-energy (i.e. the -kbT*log of the desired target distribution).
+Gaussians will then be scaled by a factor
+\f[
+e^{\beta(\tilde{F}(s)-\tilde{F}_{max})}
+\f]
+Here \f$\tilde{F}(s)\f$ is the free energy defined on the grid and \f$\tilde{F}_{max}\f$ its maximum value.
+Notice that we here used the maximum value as in ref \cite gil2016empirical
+This choice allows to avoid exceedingly large Gaussians to be added. However,
+it could make the Gaussian too small. You should always choose carefully the HEIGHT parameter
+in this case.
+The grid file should be similar to other PLUMED grid files in that it should contain
+both the target free-energy and its derivatives.
+
+Notice that if you wish your simulation to converge to the target free energy you should use
+the DAMPFACTOR command to provide a global tempering \cite dama2014well
+Alternatively, if you use a BIASFACTOR yout simulation will converge to a free
+energy that is a linear combination of the target free energy and of the intrinsic free energy
+determined by the original force field.
+
 
 */
 //+ENDPLUMEDOC
@@ -842,6 +866,11 @@ last_step_warn_grid(0)
      "Pratyush and Parrinello, J. Phys. Chem. B, 119, 736 (2015)");
   if(concurrent) log<<plumed.cite(
      "Gil-Ley and Bussi, J. Chem. Theory Comput. 11, 1077 (2015)");
+  if(targetfilename_.length()>0){
+    log<<plumed.cite("White, Dama, and Voth, J. Chem. Theory Comput. 11, 2451 (2015)");
+    log<<plumed.cite("Marinelli and Faraldo-Gómez,  Biophys. J. 108, 2779 (2015)");
+    log<<plumed.cite("Gil-Ley, Bottaro, and Bussi, submitted (2016)");
+  }
   log<<"\n";
 
 }
diff --git a/user-doc/bibliography.bib b/user-doc/bibliography.bib
index 0869142ea..7925c274a 100644
--- a/user-doc/bibliography.bib
+++ b/user-doc/bibliography.bib
@@ -2197,3 +2197,46 @@ number = {11},
 pages = {5062-5067},
 year = {2015}
 }
+
+@article{marinelli2015ensemble,
+        Author = {Marinelli, Fabrizio and Faraldo-G{\'o}mez, Jos{\'e} D},
+        Date-Added = {2015-07-24 14:22:59 +0000},
+        Date-Modified = {2015-09-27 11:05:20 +0000},
+        Journal = {Biophys. J.},
+        Number = {12},
+        Pages = {2779-2782},
+        Publisher = {Elsevier},
+        Title = {Ensemble-Biased Metadynamics: A Molecular Simulation Method to Sample Experimental Distributions},
+        Volume = {108},
+        Year = {2015}}
+
+@article{white2015designing,
+        Author = {White, Andrew and Dama, James and Voth, Gregory A},
+        Date-Added = {2015-07-24 14:23:23 +0000},
+        Date-Modified = {2015-09-27 11:08:36 +0000},
+        Journal = {J. Chem. Theory Comput.},
+        Number = {6},
+        Pages = {2451--2460},
+        Publisher = {ACS Publications},
+        Title = {Designing Free Energy Surfaces that Match Experimental Data with Metadynamics},
+        Volume = {11},
+        Year = {2015}}
+
+@article{dama2014well,
+        Author = {Dama, James F and Parrinello, Michele and Voth, Gregory A},
+        Journal = {Phys. Rev. Lett.},
+        Number = {24},
+        Pages = {240602},
+        Publisher = {APS},
+        Title = {Well-Tempered Metadynamics Converges Asymptotically},
+        Volume = {112},
+        Year = {2014}}
+
+
+@misc{gil2016empirical,
+  title={Empirical corrections to the Amber RNA force field with Target Metadynamics},
+  author={Gil-Ley, Alejandro and Bussi, Giovanni},
+  note={submitted}
+}
+
+
-- 
GitLab