Merge remote-tracking branch 'origin/v2.5' into v2.5

user-doc/VES.md

@@ -109,7 +109,7 @@ Variationally Enhanced Sampling:
 
 \par Tuesday February 14
 
-\ref lugano-1 "Tutorial 1": Introduction to PLUMED and analyzing molecular simulations
+\ref marvel-1 "Tutorial 1": Introduction to PLUMED and analyzing molecular simulations
 
 \par Wednesday February 15
 
@@ -122,7 +122,7 @@ Variationally Enhanced Sampling:
 \ref ves-lugano2017-ves2 "Tutorial 4": Further on variationally enhanced sampling
 
 Tutorial 5: Advanced collective variables
-- \ref lugano-2 "Path CVs"
+- \ref marvel-2 "Path CVs"
 - \ref belfast-10 "Multicolvar"
 - \ref belfast-3 "Dimensionality reduction"
 

user-doc/tutorials/aa-lugano-4.txt

@@ -580,3 +580,5 @@ by reading https://arxiv.org/abs/1812.08213.
 link: @subpage lugano-4 
 
 description: Calculating error bars
+
+additional-files: lugano-4

user-doc/tutorials/aa-lugano-6c.txt

@@ -60,7 +60,7 @@ use the plumed \ref driver and VMD to choose to water molecule relatively far ap
 \section  lugano-6c-ex-2 Exercise 2: Proton transfer
 
 In this exercise you are challanged to
-- Select two water molecule to be kept far apart using UPPER_WALLS and the distance between their two oxygen atoms.
+- Select two water molecule to be kept far apart using \ref LOWER_WALLS and the distance between their two oxygen atoms.
 - Use the distances of an hydrogen from both oxygens to setup a first \ref METAD calculation to study the proton transfer between the selected water molecules
 - Test more complex CVs maybe taking into accout the role of the other molecules.
 - Think how to study proton transfer in a general way instead than between two specif water molecules and using a specific hydrongen.