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Repository with conda recipes for LAMMPS, GROMACS, etc (WIP)

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# Conda packages for GROMACS and LAMMPS

## Install conda

First you should install conda. In order to do so execute the commands below:

````
wget -c https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
# on MacOS replace with:
# wget -c https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda.sh
bash ./miniconda.sh -b -f -p /path/to/conda
export PATH="/path/to/conda/bin:$PATH"
source activate base
````

Here `/path/to/conda` should be the path where you want to install conda. You can choose it in your home so that you will have write permission to it.

You might want to use a separate environment just for the Lugano tutorial. You can do it using the following commands

````
conda create --name lugano-tutorials
source activate lugano-tutorials
````

The second command should be repeated every time you open a new shell.
In case you have already conda installed, by working in a separate environment you will make sure that there
will not be interference between packages specifically needed for this tutorial and packages that you have already installed.

## Install PLUMED

This command installs a special version of PLUMED 2.5.1 that also includes the optional dimred module.

````
conda install -c plumed/label/lugano -c conda-forge plumed
````

Make sure you include the two channels in the right order, so that `plumed/label/lugano` has the priority, since the version
of PLUMED available on conda-forge does not include the dimred module.
On OSX, the command above should install the following packages:

````
  gsl                conda-forge/osx-64::gsl-2.5-ha2d443c_0
  libblas            conda-forge/osx-64::libblas-3.8.0-10_openblas
  libcblas           conda-forge/osx-64::libcblas-3.8.0-10_openblas
  libcxx             conda-forge/osx-64::libcxx-8.0.0-4
  libcxxabi          conda-forge/osx-64::libcxxabi-8.0.0-4
  libgfortran        conda-forge/osx-64::libgfortran-3.0.1-0
  liblapack          conda-forge/osx-64::liblapack-3.8.0-10_openblas
  libopenblas        conda-forge/osx-64::libopenblas-0.3.6-hd44dcd8_4
  llvm-openmp        conda-forge/osx-64::llvm-openmp-8.0.0-h770b8ee_0
  openblas           conda-forge/osx-64::openblas-0.3.6-hd44dcd8_4
  plumed             plumed/label/lugano/osx-64::plumed-2.5.1-h0a44026_3
  xdrfile            conda-forge/osx-64::xdrfile-1.1.4-h01d97ff_0
  zlib               conda-forge/osx-64::zlib-1.2.11-h01d97ff_1005
````

Again, notice that the `plumed` package comes from `plumed/label/lugano`, whereas all the libraries come from `conda-forge`.

## Install GROMACS

This command installs a special version of GROMACS 2018.6 pre-patched with PLUMED.
Patching is done in runtime mode, and should by default pick the PLUMED library installed
on conda in the same environment, using the command above.

````
conda install -c plumed/label/lugano -c conda-forge gromacs
````

On OSX, the command above should install the following packages:

````
  fftw               conda-forge/osx-64::fftw-3.3.8-mpi_mpich_h6e18f22_1006
  gromacs            plumed/label/lugano/osx-64::gromacs-2018.6-h2b26ce3_0
  icu                conda-forge/osx-64::icu-58.2-h0a44026_1000
  libhwloc           conda-forge/osx-64::libhwloc-1.11.9-0
  libiconv           conda-forge/osx-64::libiconv-1.15-h01d97ff_1005
  libxml2            conda-forge/osx-64::libxml2-2.9.9-hd80cff7_1
  mpi                conda-forge/osx-64::mpi-1.0-mpich
  mpich              conda-forge/osx-64::mpich-3.2.1-ha90c164_1013
  xz                 conda-forge/osx-64::xz-5.2.4-h1de35cc_1001
````

Notice that MPI is installed as a requirement of one of the libraries used by GROMACS, but GROMACS itself
will be installed in non-MPI version (with openMP parallelism enabled).

## Install LAMMPS

This command installs a special version of LAMMPS 2019, June, pre-patched with PLUMED.
Patching is done in runtime mode, and should by default pick the PLUMED library installed
on conda in the same environment, using the command above.

````
conda install -c plumed/label/lugano -c conda-forge lammps
````

On OSX, the command above should install the following packages:

````
  lammps             plumed/label/lugano/osx-64::lammps-2019.6.5-h2b26ce3_0
  libjpeg-turbo      conda-forge/osx-64::libjpeg-turbo-2.0.2-h1de35cc_0
  libpng             conda-forge/osx-64::libpng-1.6.37-h2573ce8_0
````

## Install other software that you will need

Using conda you might also install other software that will be used during the workshop.
You will likely need these python packages:

````
conda install -c conda-forge numpy
conda install -c conda-forge scipy
````

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