fixing typos and minor stuff - still one exercise missing

user-doc/tutorials/a-trieste-4.txt

@@ -3,9 +3,9 @@
 
 \section trieste-4-aims Aims
 
-The aim of this tutorial is to train the users to perform 
+The aim of this tutorial is to train users to perform 
 metadynamics simulations with PLUMED, analyze the results, calculating free-energies as a function 
-of the collective variables used and estimating the associated error.
+of the collective variables used, and estimating the associated error.
 
 \section trieste-4-objectives Objectives
 
@@ -20,14 +20,14 @@ Once this tutorial is completed students will be able to:
 \section trieste-4-resources Resources
 
 The \tarball{trieste-4} for this project contains the following files:
-- diala.pdb : a PDB file for alanine dipeptide in vacuo
-- topol.tpr : GROMACS run file to run MD of alanine dipeptide
-- XXXX.py   : a python script to block analysis
+- diala.pdb: a PDB file for alanine dipeptide in vacuo
+- topol.tpr: a GROMACS run file to perform MD of alanine dipeptide
+- XXXX.py: a python script to perform error analysis
 
 This tutorial has been tested on a pre-release version of version 2.4. However, it should not take advantage
 of 2.4-only features, thus should also work with version 2.3.
 
-\note We suggest to run the three exercizes in separate directories
+\note We suggest to run the three exercizes in three separate directories. For Exercize 3, you will need the output of the first two exercizes, so don't delete it!
  
 \section trieste-4-intro Introduction
 
@@ -103,7 +103,8 @@ Additional information can be found in the several review papers on metadynamics
 
 \endhidden
 
-We will play with a toy system, alanine dipeptide simulated in vacuo using the AMBER99SB force field (see Fig. \ref trieste-4-ala-fig).
+We will play with a toy system, alanine dipeptide simulated in vacuo using the AMBER99SB-ILDN 
+force field (see Fig. \ref trieste-4-ala-fig).
 This rather simple molecule is useful to benchmark data analysis and free-energy methods.
 This system is a nice example because it presents two metastable states separated by a high free-energy barrier.
 It is conventional use to characterize the two states in terms of Ramachandran dihedral angles, which are denoted with \f$ \Phi \f$ and \f$ \Psi \f$ in Fig. \ref trieste-4-transition-fig .
@@ -117,6 +118,8 @@ It is conventional use to characterize the two states in terms of Ramachandran d
 
 \section trieste-4-ex-1 Exercize 1: my first metadynamics calculation
 
+\subsection trieste-4-ex-1a Exercize 1a: setup and run 
+
 In this excercise we will setup and perform a well-tempered metadynamics run using the backbone dihedral \f$ \phi \f$
 as collective variable. During the calculation, we will also monitor the behavior of the other backbone dihedral \f$ \psi \f$.
 
@@ -160,9 +163,9 @@ In case you do not provide any information about bin size (neither GRID_BIN nor
 and if Gaussian width is fixed, PLUMED will use 1/5 of the Gaussian width as grid spacing.
 This default choice should be reasonable for most applications.
 
-Once your `plumed.dat` file is complete, you can run a XX-ns long metadynamics simulations with the following command
+Once your `plumed.dat` file is complete, you can run a 10-ns long metadynamics simulations with the following command
 \verbatim
-> gmx mdrun -s topol.tpr -plumed plumed.dat 
+> gmx mdrun -s topol.tpr -nsteps 5000000 -plumed plumed.dat 
 \endverbatim
 
 During the metadynamics simulation, PLUMED will create two files, named COLVAR and HILLS.
@@ -206,6 +209,8 @@ of the Gaussian height is higher than the initial height specified in the input
 In fact, this column reports the height of the Gaussian rescaled by the pre-factor that
 in well-tempered metadynamics relates the bias potential to the free energy.
 
+\subsection trieste-4-ex-1b Exercize 1b: estimating the free energy 
+
 One can estimate the free energy as a function of the metadynamics CVs directly from the metadynamics
 bias potential. In order to do so, the utility \ref sum_hills should be used to sum the Gaussians
 deposited during the simulation and stored in the HILLS file.  
@@ -215,7 +220,7 @@ To calculate the free energy as a function of \f$ \phi \f$, it is sufficient to
 plumed sum_hills --hills HILLS
 \endverbatim
 
-The command above generates a file called fes.dat in which the free-energy surface as function
+The command above generates a file called `fes.dat` in which the free-energy surface as function
 of \f$ \phi \f$ is calculated on a regular grid. One can modify the default name for the free energy file,
 as well as the boundaries and bin size of the grid, by using the following options of \ref sum_hills :
 
@@ -234,8 +239,8 @@ The result should look like this:
 
 To assess the convergence of a metadynamics simulation, one can calculate the estimate of the free energy as a function
 of simulation time. At convergence, the reconstructed profiles should be similar.
-The option --stride should be used to give an estimate of the free energy every N Gaussians deposited, and
-the option --mintozero can be used to align the profiles by setting the global minimum to zero.
+The option \-\-stride should be used to give an estimate of the free energy every N Gaussians deposited, and
+the option \-\-mintozero can be used to align the profiles by setting the global minimum to zero.
 If we use the following command line:
 
 \verbatim
@@ -252,7 +257,7 @@ These two qualitative observations:
 - the system is diffusing efficiently in the collective variable space (Figure \ref trieste-4-phi-fig) 
 - the estimated free energy does not change significantly as a function of time (Figure \ref trieste-4-metad-phifest-fig) 
 
-suggest that the simulation is converged. 
+suggest that the simulation most likely converged. 
 
 \warning The fact that the Gaussian height is decreasing to zero should not be used as a measure of convergence
 of your metadynamics simulation!
@@ -263,16 +268,16 @@ reconstructed free-energy profile, as explained in the last exercize
 
 \section trieste-4-ex-2 Exercize 2: playing with collective variables
 
-In this exercise, we will run a well-tempered metadynamics simulation on alanine dipeptide in vacuum, this time
+In this exercize, we will run a well-tempered metadynamics simulation on alanine dipeptide in vacuum, this time
 using as CV the backbone dihedral \f$ \psi \f$. 
-Please complete the template `plumed.dat` file used in the previous exercise to run this calculation.
+Please complete the template `plumed.dat` file used in the previous exercize to run this calculation.
 
-Once your `plumed.dat` file is complete, you can run a XX-ns long metadynamics simulations with the following command
+Once your `plumed.dat` file is complete, you can run a 10-ns long metadynamics simulations with the following command
 \verbatim
-> gmx mdrun -s topol.tpr -plumed plumed.dat
+> gmx mdrun -s topol.tpr -nsteps 5000000 -plumed plumed.dat
 \endverbatim
 
-As we did in the previous exercise, we can use COLVAR to visualize the behavior of the CV during the simulation.
+As we did in the previous exercize, we can use COLVAR to visualize the behavior of the CV during the simulation.
 Here we will plot at the same time the evolution of the metadynamics CV \f$ \psi \f$ and of the other dihedral \f$ \phi \f$.
 
 \verbatim
@@ -282,14 +287,14 @@ gnuplot> p "COLVAR" u 1:2, "" u 1:3
 \anchor trieste-4-metad-psi-phi-fig
 \image html munster-metad-psi-phi.png "Time evolution of the dihedrals phi and psi during a 10-ns long metadynamics simulation using psi as CV."
 
-By inspecting Figure \ref trieste-4-metad-psi-phi-fig, we notice that something different happened compared to the previous exercise.
+By inspecting Figure \ref trieste-4-metad-psi-phi-fig, we notice that something different happened compared to the previous exercize.
 At first the behavior of \f$ \psi \f$ looks diffusive in the entire CV space. However, around t=1 ns, \f$ \psi \f$ 
 seems trapped in a region of the CV space in which it was previously diffusing without problems. 
 The reason is that the non-biased CV \f$ \phi \f$ after a while has jumped into a different local minima.
 Since \f$ \phi \f$ is not directly biased, one has to wait for this (slow) degree of freedom to 
 equilibrate before the free energy along \f$ \psi \f$ can converge.
 
-Try to repeat the analysis done in the previous exercise, i.e.  calculate the estimate of the free energy as a function of time,
+Try to repeat the analysis done in the previous exercize, i.e.  calculate the estimate of the free energy as a function of time,
 first step to assess the convergence of this metadynamics simulation.
 
 \section trieste-4-ex-3 Exercize 3: quantifying the error in free-energy reconstructions