Updated user manual plumed -> PLUMED

To be consistent with the paper, plumed is always capital letters.
I also changed 2.0 -> 2 and 1.0 -> 1 for sake of generality

user-doc/Analysis.txt

@@ -2,7 +2,7 @@
 
 \page Analysis Analysis
 
-Once you have calculated a number of collective variables plumed allows you to either analyse
+Once you have calculated a number of collective variables PLUMED allows you to either analyse
 your trajectory.  The list of available on-the-fly analysis tools contains:
 
 @ANALYSIS@

user-doc/Bias.txt

@@ -2,7 +2,7 @@
 
 \page Bias Bias
 
-Once you have calculated a number of collective variables plumed allows you to
+Once you have calculated a number of collective variables PLUMED allows you to
 run a number of enhanced sampling algorithms.
 The list of available enhanced sampling algorithms contains: 
 
@@ -11,7 +11,7 @@ The list of available enhanced sampling algorithms contains:
 Methods, such as \ref METAD, that introduce a history dependent bias can be restarted 
 using the \subpage RESTART keyword
 
-You can also use plumed in conjunction with VMD's interactive MD module by taking
+You can also use PLUMED in conjunction with VMD's interactive MD module by taking
 advantage of the \subpage IMD action.
 
 */

user-doc/Colvar.txt

@@ -6,13 +6,13 @@ Chemical systems contain an enormous number atoms, which, in most cases makes it
 us to understand anything by monitoring the atom postions directly.  Consquentially,
 we introduce Collective variables (CVs) that describe the chemical processes we are 
 interested in and monitor these simpler quantities instead.  These CVs are used in all of the methods 
-implemented in plumed - they're values can be monitored using \ref PRINT, \ref Function of them can be calculated
-or they can be analyzed or biased using the \ref Analysis and \ref Bias "Biasing" methods implemented in plumed.  
-Before doing any of these things however we first have to inform plumed how to calculate them.    
+implemented in PLUMED - they're values can be monitored using \ref PRINT, \ref Function of them can be calculated
+or they can be analyzed or biased using the \ref Analysis and \ref Bias "Biasing" methods implemented in PLUMED.  
+Before doing any of these things however we first have to inform PLUMED how to calculate them.    
  
 \section atomSpecs Specifying Atoms
 
-The vast majority of the CVs implemented in plumed are calculated from a list of atom positions.  Within plumed
+The vast majority of the CVs implemented in PLUMED are calculated from a list of atom positions.  Within PLUMED
 atoms are always specified according to their numerical indices in the molecular dynamics input file.  This can
 be done either using a comma separated list of numbers or, if a long list atom of contiguous atoms is required, 
 by using the shortcut 10-100, which specifies all the atom indexes between 10 and 100 (including 10 and 100).  So for example:
@@ -43,7 +43,7 @@ In addition, for certain colvars, pdb files can be read in using the following k
 
 @TOPOLOGY@
 
-The read in pdb files are used by plumed to define things like residues, the backbone atoms and so on.  These can then be
+The read in pdb files are used by PLUMED to define things like residues, the backbone atoms and so on.  These can then be
 used within the input to colvars to make inputting the lists of atoms involved more straightforward.  Documentation for 
 how these shortcuts can be used can be found in the documentation for the various CVs.
 
@@ -77,15 +77,15 @@ If you don't want to calculate CVs from the virtual atom.  That is to say you ju
 PLUMED is designed so that for the majority of the CVs implemented the periodic boundary conditions are treated 
 in the same manner as they would be treated in the host code.  In some codes this can be problematic when the colvars
 you are using involve some property of a molecule.  These codes allow the atoms in the molecules to become separated by 
-periodic boundaries, a fact which plumed could only deal with were the topology passed from the MD code to plumed.  Making this
+periodic boundaries, a fact which PLUMED could only deal with were the topology passed from the MD code to PLUMED.  Making this
 work would involve a lot laborious programming and goes against our original aim of having a general patch that can be implemented 
 in a wide variety of MD codes.  Consequentially, we have implemented a more pragmatic solution to this probem - the user specifies
-in input any molecules (or parts of molecules) that must be kept in tact throughout the simulation run.  In plumed 1.0 this was done
-using the ALIGN_ATOMS keyword.  In plumed 2.0 the same effect can be acchieved using the \subpage WHOLEMOLECULES command.
+in input any molecules (or parts of molecules) that must be kept in tact throughout the simulation run.  In PLUMED 1 this was done
+using the ALIGN_ATOMS keyword.  In PLUMED 2 the same effect can be acchieved using the \subpage WHOLEMOLECULES command.
 
 \section cvavail CV Documentation
 
-The following list contains all the colvars that are currently implemented in plumed 2.0.
+The following list contains all the colvars that are currently implemented in PLUMED 2.
 
 @COLVAR@
 
@@ -94,16 +94,16 @@ The following list contains all the colvars that are currently implemented in pl
 Often you do not need one of the collective variables described in the previous section.  What you want instead is a 
 function of a distribution of collective variables of a particular type.  For instance you might need to calculate a 
 minimum distance or the number of coordination numbers greater than a 3.0.  To avoid dupilcating the code to calculate
-an angle or distance many times and to make it easier to implement very complex collective variables plumed provides
+an angle or distance many times and to make it easier to implement very complex collective variables PLUMED provides
 these sort of collective variables using so-called MultiColvars.  MultiColvars are named in this way because a single
-plumed action can be used to calculate a number of different collective variables.  For instance the \ref DISTANCES
+PLUMED action can be used to calculate a number of different collective variables.  For instance the \ref DISTANCES
 action can be used to calculate the minimum distance, the number of distances less than a certain value, the number of
-distances within a certain range...  Descriptions as to how to use plumed to calculate these kinds of CVs are given
+distances within a certain range...  Descriptions as to how to use PLUMED to calculate these kinds of CVs are given
 below:
 
 @MCOLVAR@   
 
-To instruct plumed to calculate a multicolvar you give an instruction that looks something like this:
+To instruct PLUMED to calculate a multicolvar you give an instruction that looks something like this:
 
 \verbatim
 NAME <atoms involved> <parameters> <what am I calculating> TOL=0.001 LABEL=label

user-doc/Functions.txt

@@ -3,7 +3,7 @@
 
 When performing biased dynamics or analysing a trajectory you may wish to analyse/bias the value of
 some function of a set of collective variables rather than the values of the collective variables
-directly.  You can do this with plumed by using any one of the following list of functions: 
+directly.  You can do this with PLUMED by using any one of the following list of functions: 
 
 @FUNCTION@
 

user-doc/Glossary.txt

@@ -3,7 +3,7 @@
 @page glossary Glossary of Actions 
 
 The following page contains an alphabetically ordered list of all the Actions and command line tools 
-that are available in plumed 2.0. For lists of Actions classified in accordance with the 
+that are available in PLUMED 2. For lists of Actions classified in accordance with the 
 particular tasks that are being performed see:
 
 - \ref Colvar

user-doc/Installation.txt

@@ -2,9 +2,9 @@
 
 \page Installation Installation
 
-\section CompilingPlumed Compiling Plumed
+\section CompilingPlumed Compiling PLUMED
 
-Plumed does not yet have any automatic configuration procedure and most of the 
+PLUMED does not yet have any automatic configuration procedure and most of the 
 decisions should be taken by the user. As a first step configure with the command:
 \verbatim
 > ./configure
@@ -14,10 +14,10 @@ You will have to choose among a set of available preconfigured files.
 Choose the one closest to your machine, then edit the resulting
 Makefile.conf file. Notable variables there:
 - LIBS : these are the libraries needed when patching an MD code; typically only "-ldl" (needed to have functions for dynamic loading).
-- DYNAMIC_LIB : these are the libraries needed to compile the plumed
+- DYNAMIC_LIB : these are the libraries needed to compile the PLUMED
 library (e.g. -L/path/to/matheval -lmatheval etc). Notice that for the
-plumed shared library to be compiled properly these should be dynamic
-libraries. Also notice that plumed requires BLAS and LAPACK library;
+PLUMED shared library to be compiled properly these should be dynamic
+libraries. Also notice that PLUMED requires BLAS and LAPACK library;
 see \ref BlasAndLapack for further info.
 - CPPFLAGS : add here definition needed to enable specific optional functions;
 e.g. use -D__PLUMED_HAS_MATHEVAL to enable matheval library
@@ -26,15 +26,15 @@ e.g. use -D__PLUMED_HAS_MATHEVAL to enable matheval library
 just set this variable to a blank ("SOEXT=").
 
 Also notice that a  new file sourceme.sh
-appears in the main plumed directory.
+appears in the main PLUMED directory.
 This file should be "sourced" (presently only working for bash shell)
-if you want to use plumed *without installin it* (i.e. from the compilation
+if you want to use PLUMED *without installin it* (i.e. from the compilation
 directory. It is a good idea to source it now:
 \verbatim
 > source sourceme.sh
 \endverbatim
 
-Then compile plumed
+Then compile PLUMED
 \verbatim
 > make -j 4
 \endverbatim
@@ -45,7 +45,7 @@ a "plumed" executable should be in your path. Try to type
 > plumed -h
 \endverbatim
 
-You can also check if plumed is correctly compiled performing our regression tests.
+You can also check if PLUMED is correctly compiled performing our regression tests.
 Be warned that some of them just fails because of the different numerical accuracy of different machines.
 \verbatim
 > cd regtest
@@ -57,20 +57,20 @@ You can check with exact version they will use with the command
 > which plumed
 \endverbatim
 This means that if you do not source "sourceme.sh" file, tests will fails. Moreover, in case you have
-another version of plumed installed somewhere regtests might use that one instead
+another version of PLUMED installed somewhere regtests might use that one instead
 of the just-compiled one.
 
 Also notice that the compiled executable, which now sits in src/lib/plumed, relies
 on other resource files present in the compilation directory.
 This directory should thus stay in the correct place, and one should not
-rename or delete it. The path to the plumed root directory is indeed
+rename or delete it. The path to the PLUMED root directory is indeed
 hardcoded in the plumed executable and can be verified with
 \verbatim
 > plumed info --root
 \endverbatim
 In case you try to use the plumed executable without the compilation
 directory in place (e.g. you move away the src/lib/plumed static executable
-and delete or rename the compilation directory) plumed will 
+and delete or rename the compilation directory) PLUMED will 
 not work correctly and will give you an
 error message
 \verbatim
@@ -82,7 +82,7 @@ You can force plumed to run anyway using the option --standalone-executable:
 > plumed --standalone-executable help
 \endverbatim
 Anyway, many features will not be available in this way.
-This is currently the only way to use a plumed static executable on Windows.
+This is currently the only way to use a PLUMED static executable on Windows.
 
 \section BlasAndLapack BLAS and LAPACK
 
@@ -110,14 +110,14 @@ in configuration file).
 
 \section Installing Installing PLUMED
 
-It might be convenient to install plumed in a predefined location.
+It might be convenient to install PLUMED in a predefined location.
 This will allow you to remove the original compilation directory,
-or to recompile e.g. a different plumed version in the same place.
+or to recompile e.g. a different PLUMED version in the same place.
 Notice that installation *is optional*. Even from the compilation
 directory, if environment is properly set (see sourceme.sh file)
-plumed should work.
+PLUMED should work.
 
-To install plumed one should first decide the location. Just set
+To install PLUMED one should first decide the location. Just set
 the environment variable PLUMED_PREFIX, then type "make install"
 \verbatim
 > export PLUMED_PREFIX=$HOME/opt
@@ -125,32 +125,32 @@ the environment variable PLUMED_PREFIX, then type "make install"
 \endverbatim
 If PLUMED_PREFIX is not set, it will be assumed to be /usr/local.
 The install command should be executed with root permissions (e.g. "sudo make install")
-in case you want to install plumed on a system directory.
+in case you want to install PLUMED on a system directory.
 An almost full copy of the compilation directory will
 be installed into $PLUMED_PREFIX/lib/plumed/ directory. A link to the proper
-plumed executable will be set up in $PLUMED_PREFIX/bin,
-plumed include files will be copied to $PLUMED_PREFIX/include/plumed
-and plumed libraries will be linked to $PLUMED_PREFIX/lib.
+PLUMED executable will be set up in $PLUMED_PREFIX/bin,
+PLUMED include files will be copied to $PLUMED_PREFIX/include/plumed
+and PLUMED libraries will be linked to $PLUMED_PREFIX/lib.
 
 One should then set the environment properly. We suggest to do it using
 the module framework (http://modules.sourceforge.net). An ad hoc generated
-module file for plumed can then be found in $PLUMED_PREFIX/lib/plumed/src/lib/modulefile
+module file for PLUMED can then be found in $PLUMED_PREFIX/lib/plumed/src/lib/modulefile
 Just edit it at your will and put it in your modulefile directory.
-This will also allow you to install several plumed versions alongside and
+This will also allow you to install several PLUMED versions alongside and
 switch among them. If you do not want to use modules, you can 
 still have a look at the modulefile we did so as to know which
-environment variables should be set for plumed to work correctly.
+environment variables should be set for PLUMED to work correctly.
 
 If the environment is properly configured one should be able to do
 the following things:
 - use "plumed" executable from the command line. this is also possible before installing.
-- link against the plumed library using "-lplumed" flag for the linker. this allows
-  one to use plumed library in general purpose programs
-- use the plumed internal functionalities (C++ classes) including
+- link against the PLUMED library using "-lplumed" flag for the linker. this allows
+  one to use PLUMED library in general purpose programs
+- use the PLUMED internal functionalities (C++ classes) including
   header files such as "#include <plumed/tools/Vector.h>". this is also usefule to
-  exploit the plumed library in general purpose programs
+  exploit the PLUMED library in general purpose programs
 
-As a final note, one may want to install several plumed version
+As a final note, one may want to install several PLUMED version
 alongside without using modules.
 An alternative is to also define the environment variable PLUMED_LIBSUFFIX. E.g. with
 \verbatim
@@ -159,13 +159,13 @@ An alternative is to also define the environment variable PLUMED_LIBSUFFIX. E.g.
 > make install
 \endverbatim
 will install plumed executable with name "plumed-v2.0". All the other files will be renamed accordingly,
-e.g. the plumed library will be loaded with "-lplumed-v2.0" and the plumed header files
+e.g. the PLUMED library will be loaded with "-lplumed-v2.0" and the PLUMED header files
 will be included with "#include <plumed-v2.0/tools/Vector.h>. This trick is useful if you
 do not want to set up modules, but we think using modules (see above) is more flexible.
 
 \section Patching Patching your MD code
 
-At the present times plumed can be added to the following list of codes:
+At the present times PLUMED can be added to the following list of codes:
 
 @CODES@
 
@@ -190,16 +190,17 @@ There are different options when patching, check them using
 > plumed patch --help
 \endverbatim
 Interesing ones:
-- --shared allows you to link plumed as a shared library. when plumed is updated, there will be no need to recompile the MD code
-- --runtime allows you to choose the location of the plumed library at runtime, setting the variable PLUMED_KERNEL.
-- --static (default) just link plumed as a collection of object files
+- --shared allows you to link PLUMED as a shared library. when PLUMED is updated, there will be no need to recompile the MD code
+- --runtime allows you to choose the location of the PLUMED library at runtime, setting the variable PLUMED_KERNEL.
+- --static (default) just link PLUMED as a collection of object files
 
 A note for cross compiling: in case you are compiling an executable from a different machine, then
 "plumed" executable will not be available in the compilation environment. You can thus use the following command
 \verbatim
 > plumed-patch
 \endverbatim
-as a replacement of "plumed patch". This trick only works with "patch" subcommand (e.g. no "plumed-help" available...).
+as a replacement of "plumed patch". This trick only works with those commands which are implemented as pure scripts
+(e.g. there is no "plumed-help" available...).
 
 If your MD code is not supported, you may want to implement an interface for
 it. Refer to the <a href="../../developer-doc/html/index.html"> developer

user-doc/Intro.txt

 /**
 \mainpage Introduction
 
-Plumed is a plugin that works with a large number of molecular dynamics codes.  It can be used
+PLUMED is a plugin that works with a large number of molecular dynamics codes.  It can be used
 to analyse features of the dynamics on-the-fly or to perform a wide variety of free energy methods.
-The original plumed 1.0 was highly successful and had over 1000 users.  Plumed 2.0 constitues an 
+The original PLUMED 1 was highly successful and had over 1000 users.  PLUMED 2 constitues an 
 extensive rewrite of the original in a way that makes it more modular and thus easier to implement 
 new methods, more straightforward to add it to MD codes and hopefully simpler to use.  
 This is the user manual -  if you want to modify PLUMED or to understand how it works internally, have a look at the 
 <a href="../../developer-doc/html/index.html"> developer manual </a>.  Alternatively, to look at a list of the new 
-features available in plumed 2.0 and to work out how to install plumed 2.0 in your MD code check out:
+features available in PLUMED 2 and to work out how to install PLUMED 2 in your MD code check out:
 
 - \subpage WhatsNew
 - \subpage Installation 
 
 See also \ref CHANGES-2-0
 
-
 \section qintro A quick introduction
 
-To run plumed 2.0 you need to provide one input file.  In this file you specify what it
-is that plumed should do during the course of the run.  Typically this will involve calculating 
+To run PLUMED 2 you need to provide one input file.  In this file you specify what it
+is that PLUMED should do during the course of the run.  Typically this will involve calculating 
 one or more collective variables, perhaps calculating a function of these CVs
  and then doing some analysis of values of your collective variables/functions or running
 some free energy method.  Details as to how to perform all these tasks and how to use the various trajectory
-analsyis tools that come with plumed are given in:
+analsyis tools that come with PLUMED are given in:
 
 - \subpage Colvar
 - \subpage Function
 - \subpage Analysis
 - \subpage Bias
 
-Plumed can be used in one of two ways.  It can be incorporated into any one of the MD codes listed on the
+PLUMED can be used in one of two ways.  It can be incorporated into any one of the MD codes listed on the
 \ref Installation page and used to analyse or bias a molecular dynamics run on the fly.  Alternatively, one
 can use it as a standalone tool for postprocessing the results from molecular dynamics or enhanced sampling calculations.
-To use plumed in this second way you will issue a command something like:
+To use PLUMED in this second way you will issue a command something like:
 
 \verbatim
 plumed <toolname> <list of input flags for that tool>
 \endverbatim
 
-The following is a list of the various standalone tools that plumed contains.
+The following is a list of the various standalone tools that PLUMED contains.
 
 @TOOLS@
 
-For all these tools and to use plumed as a pluggin in an MD calculation you will need an input file.  Within
-this input file every line is an instruction for plumed to perform some particular action.  This could be
+For all these tools and to use PLUMED as a plugin in an MD calculation you will need an input file.  Within
+this input file every line is an instruction for PLUMED to perform some particular action.  This could be
  the calculation of a colvar, an occasional analysis of the trajectory or a biassing of the dynamics.  The first
 word in these lines specify what particular action is to be performed.  This is then followed by a number of keywords
-which provide plumed with more details as to how the action is to be performed.  These keywords are either single words
-(in which they tell plumed to do the calculation in a particular way - for example NOPBC tells plumed to not use the periodic
+which provide PLUMED with more details as to how the action is to be performed.  These keywords are either single words
+(in which they tell PLUMED to do the calculation in a particular way - for example NOPBC tells PLUMED to not use the periodic
 bounadry conditions when calculating a particular colvar) or they can be words followed by an equals sign and a comma separated 
-list - WITH NO SPACES - of numbers or characters (so for example ATOMS=1,2,3,4 tells plumed to use atom numbers 1,2,3 and 4 in 
+list - WITH NO SPACES - of numbers or characters (so for example ATOMS=1,2,3,4 tells PLUMED to use atom numbers 1,2,3 and 4 in 
 the calculation of a particular colvar). Space separated lists can be used instead of commma separated list if the entire list
 is enclosed in curly braces (e.g. ATOMS={1 2 3 4}).
 
@@ -62,7 +61,7 @@ DISTANCE ATOMS=1,2
 \endverbatim
 (see \ref DISTANCE)
 
-Then plumed will do nothing other than read in your input file.  In contrast if you do:
+Then PLUMED will do nothing other than read in your input file.  In contrast if you do:
 
 \verbatim
 DISTANCE ATOMS=1,2 LABEL=d1
@@ -70,9 +69,9 @@ PRINT ARG=d1 FILE=colvar STRIDE=10
 \endverbatim
 (see \ref PRINT)
 
-then plumed will print out the value of the distance between atoms 1 and 2 every 10 steps to the file colvar as you have told
-plumed to take the value calculated by the action d1 and to print it.  
-Notice that if a word followed by a column is added at the beginning of the line (e.g. pippo:), Plumed automatically
+then PLUMED will print out the value of the distance between atoms 1 and 2 every 10 steps to the file colvar as you have told
+PLUMED to take the value calculated by the action d1 and to print it.  
+Notice that if a word followed by a column is added at the beginning of the line (e.g. pippo:), PLUMED automatically
 removes it and adds an equivalent label (LABEL=pippo).
 Thus, a completely equivalent result can be obtained with the following shortcut:
 \verbatim
@@ -83,16 +82,16 @@ PRINT ARG=d1 FILE=colvar STRIDE=10
 Also notice that all the actions can be labeled, and that many actions besides normal collective variables can define
 one or more value, which can be then referred using the corresponding label.
 
-Actions can be referred also with POSIX regular expressions (see \ref Regex). For this you need to compile plumed with the appropriate flag.  
+Actions can be referred also with POSIX regular expressions (see \ref Regex). For this you need to compile PLUMED with the appropriate flag.  
 
 \section Units A note on units
-By default the plumed inputs and outputs quantities in the following units:
+By default the PLUMED inputs and outputs quantities in the following units:
 
 - Energy - kJ/mol
 - Length - nanometers
 - Time - picoseconds
 
-Unlike plumed 1.0 the units used are independent of the MD engine you are using.  If you want to change these units you can do this using the 
+Unlike PLUMED 1 the units used are independent of the MD engine you are using.  If you want to change these units you can do this using the 
 \subpage UNITS keyword. 
 
 Those are the essentials but there are a few other tricks that we didn't know where else to put in the manual so we stuck them here.
@@ -100,7 +99,7 @@ Those are the essentials but there are a few other tricks that we didn't know wh
 \section comments Comments
 
 If you are an organised sort of person who likes to remember what the hell you were trying to do when you ran a 
-particular simulation you might find it useful to put comments in your input file.  In plumed you can do this as 
+particular simulation you might find it useful to put comments in your input file.  In PLUMED you can do this as 
 comments can be added using a # sign.  On any given line everything after the # sign is ignored so 
 erm... yes add lines of comments or trailing comments to your hearts content as shown below (using Shakespeare is optional):
 
@@ -111,13 +110,13 @@ UPPER_WALLS ARG=d1 AT=3.0 KAPPA=3.0 LABEL=Snout # In this same interlude it doth
 \endverbatim
 (see \ref DISTANCE and \ref UPPER_WALLS)
 
-An alternative to including comments in this way is to use line starting ENDPLUMED.  Everything in the plumed input after this
+An alternative to including comments in this way is to use line starting ENDPLUMED.  Everything in the PLUMED input after this
 keyword will be ignored.
 
 \section ContinuationLines Continuation lines
 
 If your input lines get very long then editing them using vi and other such text editors becomes a massive pain in the arse.  
-We at plumed are aware of this fact and thus have provided a way of doing line continuations so as to make your life that much 
+We at PLUMED are aware of this fact and thus have provided a way of doing line continuations so as to make your life that much 
 easier - aren't we kind?  Well no not really, we have to use this code too.  Anyway, you can do continuations by using the "..." syntax
 as this makes this: 
 
@@ -139,9 +138,9 @@ DISTANCE ...
 ... DISTANCE
 \endverbatim
 
-\section includes Including other files in the plumed input
+\section includes Including other files in the PLUMED input
 
-If, for some reason, you want to spread your plumed input over a number of files you can use \subpage INCLUDE as shown below:
+If, for some reason, you want to spread your PLUMED input over a number of files you can use \subpage INCLUDE as shown below:
 
 \verbatim
 INCLUDE FILE=filename
@@ -178,10 +177,10 @@ RESTRAINT ARG=dist
 
 \section load Loading shared libraries
 
-You can introduce new functionality into plumed by placing it directly into the src directory and recompiling the 
-plumed libraries.  Alternatively, if you want to keep your code independent from the rest of plumed (perhaps
+You can introduce new functionality into PLUMED by placing it directly into the src directory and recompiling the 
+PLUMED libraries.  Alternatively, if you want to keep your code independent from the rest of PLUMED (perhaps
 so you can release it independely - we won't be offended), then you can create your own dynamic library.  To use this 
-in conjuction with plumed you can then load it at runtime by using the \subpage LOAD keyword as shown below:
+in conjuction with PLUMED you can then load it at runtime by using the \subpage LOAD keyword as shown below:
 
 \verbatim
 LOAD FILE=library.so

user-doc/Modules.txt

@@ -2,11 +2,11 @@
 
 @page mymodules Modules
 
-Plumed 2.0 is written and maintained by five core developers none of whom work full
+PLUMED 2 is written and maintained by five core developers none of whom work full
 time on the maintanence and upkeep of the code.  From our point of view it is thus 
 desirable to keep the core of the code small.  In addition, we are very keen that 
-users who contribute functionality to plumed get the plaudits that they deserve. 
-For these reasons many of plumed's more advanced functionalities are provided in 
+users who contribute functionality to PLUMED get the plaudits that they deserve. 
+For these reasons many of PLUMED's more advanced functionalities are provided in 
 modules that users can download.  To download a module you simply change to the 
 <c> plumed2/mymodules </c> directory and issue the following command:
 
@@ -14,19 +14,19 @@ modules that users can download.  To download a module you simply change to the
 ./plumed-get-module.sh <name of module>
 \endverbatim  
 
-The following optional modules can be added to plumed 2:
+The following optional modules can be added to PLUMED 2:
 
 @MODULES@
 
 \section addmodule Adding a module
 
-If you have a plumed module that you would like us to advertise on the website
+If you have a PLUMED module that you would like us to advertise on the website
 you should copy the directory structure from <c> plumed2/template-module </c> 
 as well as all the files inside that directory and place your source and regtest
 files in appropriate directories.  You are responsible for finding a suitable 
 web repository to host the code that you have developed (we use http://www.assembla.com 
-for plumed). You do not need to give us write access to your repository as ensuring that
-your code keeps working with any new release of plumed is YOUR responsibility.
+for PLUMED). You do not need to give us write access to your repository as ensuring that
+your code keeps working with any new release of PLUMED is YOUR responsibility.
 
 Once you are ready to release your code simply send any email to one of the developers
 with a txt file that contains the following information in the following format:

user-doc/Tutorials.txt

@@ -2,7 +2,7 @@
 
 @page tutorials How-tos
 
-The following pages describe how to perform a variety of tasks using plumed 2.0
+The following pages describe how to perform a variety of tasks using PLUMED 2
 
 @TUTORIALS@
 

user-doc/WhatsNew.txt

@@ -7,16 +7,16 @@
   error checking. Units are treated
   consistently, so that the plumed.dat file can be ported from on
   MD code to another.
-- Plumed is now compiled as a library, independently of the MD code.
+- PLUMED is now compiled as a library, independently of the MD code.
   This simplifies the patching procedure. Moreover, on systems where
-  this is possible, plumed library will be loaded runtime. This will
-  allow updating plumed without recompiling or relinking the MD code.
+  this is possible, PLUMED library will be loaded runtime. This will
+  allow updating PLUMED without recompiling or relinking the MD code.
 - Interfacing with MD codes is simpler. Hopefully, in the future, these
   interface will be maitained by the developers of the MD codes
-  independently from plumed developers. This will allow more MD codes
-  to be compatible with plumed.
+  independently from PLUMED developers. This will allow more MD codes
+  to be compatible with PLUMED.
 - It is now possible to develop and release collective variables,
-  free energy methods and other addons independently from plumed
+  free energy methods and other addons independently from PLUMED
   developers. This will allow more collective variables and
   free energy methods to be available.
 - Correction to the virial is computed so that constant pressure simulations
@@ -31,14 +31,14 @@
 - And many others...
 
 Caveats:
-- Plumed 2 input file (plumed.dat) has a syntax which is not
-  compatible with Plumed 1.
+- PLUMED 2 input file (plumed.dat) has a syntax which is not
+  compatible with PLUMED 1.
   Transition should be easy, but cannot
   be done just using the new version with the old input file.
-- Plumed 2 is written in C++, thus requires a C++ compiler
-- Plumed 2 may not include all the features that were available
-  in plumed 1.
+- PLUMED 2 is written in C++, thus requires a C++ compiler
+- PLUMED 2 may not include all the features that were available
+  in PLUMED 1.
 
-A tutorial explaining how to move from plumed 1 to plumed 2 is available (see \ref moving).
+A tutorial explaining how to move from PLUMED 1 to PLUMED 2 is available (see \ref moving).
 
 */