CONTENT

CHANGES/ : change log COPYING.LESSER : license Makefile : makefile PEOPLE : list of authors README : this file README.git : quick reference for git configurations/ : template configuration files configure : configuration script developer-doc : developer documentation patches : set of diff and patch scripts, needed to embed plumed in MD programs regtest : extensive set of regression tests, including reference results scripts : shell tools src : source code test : examples user-doc : user documentation

INSTALL

Extensive installation instructions are in the user documentation. Links to precompiled versions of the documentation can be found here: http://www.plumed-code.org/documentation

Needed software:

• GNU make
• c/c++ compiler
• a modern version of the "patch"
• support for POSIX library dirent.h
• xxd (present in most unix distributions)

Suggested software (libraries are checked during configure and enabled if available):

• optimized blas and lapack libraries, can be replaced by an internal version if not available
• MPI library to run parallel simulations
• VMD molfile plugins (www.ks.uiuc.edu/Research/vmd/plugins) to read arbitrary file formats, can be replaced by an internal version supporting a few formats if not available
• matheval library (www.gnu.org/software/libmatheval) to use algebraic collective variables
• doxygen (www.doxygen.org) to build user manual
• latex to build the user manual - used by doxygen
• graphviz (www.graphviz.org) to show class hierarchy in developer manual - used by doxygen

Quick compilation instructions:

• configure for your system:

  ./configure --prefix=$HOME/opt

• if necessary, edit Makefile.conf
• configure your environment

  source ./sourceme.sh

• compile plumed

  make

• the "plumed" executable should be now in the path

  plumed help

• compile the manuals

  make doc

The starting point for user documentation is user-doc/html/index.html

The starting point for developer documentation is developer-doc/html/index.html

• To install plumed in $HOME/opt (set during configure):

  umask 022 make install

• A sample modulefile with environment variable will be placed in $HOME/opt/lib/plumed/src/lib/modulefile
• Path to installed documentation can be found with command

  plumed info --user-doc

GIT VERSION

Several branches and tags are stored on the git repository.

Branches named v2.X correspond to release branches.

Master branch may contain non tested features and is not expected to be used by non-developers. It is typically containing features that will be available on the next release.

Tags named v2.XbY correspond to beta releases - use with care Tags named v2.X.Y correspond to official releases - use the latest available.

To report problems found on beta or official releases, use the normal plumed-users mailing list. Just state exactly which version you are using.

To report problems found on master branch, use the plumed2-git mailing list. This is also the correct place for discussions about new features etc. When reporting please provide the git hash (get it with "git rev-parse HEAD").