diff --git a/user-doc/tutorials/belfast-8.txt b/user-doc/tutorials/belfast-8.txt index 57e7a01626858c5cb9e67767283dddbd2caad56f..1adb7b7e0d7c6a5c09af5f092fb88943e9050c0d 100644 --- a/user-doc/tutorials/belfast-8.txt +++ b/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 diff --git a/user-doc/tutorials/belfast-9a.txt b/user-doc/tutorials/belfast-9a.txt index 922cfaf36b4cb7fe73a9439c9f52c9662adc62fc..9e8d1c951203dcd18f086515800efef8d8b79d9a 100644 --- a/user-doc/tutorials/belfast-9a.txt +++ b/user-doc/tutorials/belfast-9a.txt @@ -1,6 +1,57 @@ /** \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