belfast 8 and 9a

user-doc/tutorials/belfast-8.txt

@@ -296,7 +296,16 @@ plumed.dat.#
 INCLUDE FILE=plumed-common.dat
 
 METAD ...
-ARG=cv2,cv3 SIGMA=0.3,0.3 HEIGHT=0.2 PACE=100 LABEL=mw GRID_MIN=-pi,-pi GRID_MAX=pi,pi GRID_BIN=200,200
+LABEL=mw 
+ARG=cv2,cv3 
+SIGMA=0.3,0.3 
+HEIGHT=0.2 
+PACE=100
+BIASFACTOR=8
+TEMP=300 
+GRID_MIN=-pi,-pi 
+GRID_MAX=pi,pi 
+GRID_BIN=200,200
 WALKERS_MPI
 ... METAD
 

user-doc/tutorials/belfast-9a.txt

 /**
 \page belfast-9 Belfast tutorial: NMR constraints
 
+\section Aims
+This tutorial is about the use of experimental data, in particular NMR data, either as collective variables or as replica-averaged
+restraints in MD simulations. While the first is a just a simple extension of what we have been already doing in previous tutorials,
+the latter is an approach that can be used to increase the quality of a force-field in describing the properties of a specific system.
+
+\section belfast-9-lo Learning Outcomes
+
+Once this tutorial is completed students will:
+- know multiple ways of using experimental data in MD simulations
+- know how to use replica-averaged restrained MD simulations
+
+\section Resources
+
+\section Instructions
+
+\subsection expdata Experimental data as Collective Variables
+
+In the former tutorials it has been often discussed the possibility of measuring a distance with respect to a structure representing
+some kind of state for a system, i.e. \ref belfast-5. An alternative possibility is to use as a reference a set of experimental data
+that represent a state and measure the current deviation from the set. In plumed there are currently implemented the following NMR
+experimental observables: Chemical Shifts (only for proteins) \ref CS2BACKBONE and \ref CH3SHIFTS, \ref NOE distances and Residual Dipolar
+couplings \ref RDC. In addition \ref NOE collective variable can be also used for PRE distances and 3J Couplings will be implemented
+shortly. Among the above listed collective variables those based on chemical shifts make use of an external library, ALMOST, that  must
+be downloaded and compiled separately. In addition plumed must be configured in such a way to link ALMOST. Detailed instructions on how
+to compile PLUMED with ALMOST can be found in \ref CS2BACKBONE.
+
+In the following we will write the CS2BACKBONE collective variable that has been used in Gratana et al. (2013).
+
+\verbatim
+prot: GROUP ATOMS=1-862
+WHOLEMOLECULES ENTITY0=prot
+
+cs: CS2BACKBONE ATOMS=prot DATA=data FF=a03_gromacs.mdb NRES=56 FLAT=1.0 WRITE_CS=50 
+
+
+
+PRINT ARG=cs FILE=COLVAR STRIDE=100
+
+ENDPLUMED
+\endverbatim 
+
+
+
+\subsection replica Replica-Averaged Restrained Simulations 
+
+NMR data, as all the equilibrium experimental data, are the result of a measure over an ensemble of structures and over time.
+In principle a "perfect" molecular dynamics simulations, that is a simulations with a perfect force-field and a perfect sampling
+can predict the outcome of an experiments in a quantitative way. Actually in most of the cases obtaining a qualitative agreement
+is already a lucky outcome.
+
+
 */
 
 link: @subpage belfast-9