In this repository we report a brief guide on how to install the software needed for PLUMED Masterclass, 2022 series. Notice that different Masterclasses might require different software versions. Our recommendation is to use conda. Unfortunately we can only provide precompiled conda packages for x64 architecture, Linux and MacOS. This means that if you want to run the exercise on a different architecture (e.g., a new Mac with a ARM processor) you should install the software on your own.
First, make sure conda is installed by typing:
conda
If the command is not found, please refer to these instructions to install conda on your machine. Alternatively, if you use the Homebrew package manager, you can install conda with:
brew install --cask anaconda
# add this line to your .bashrc
export PATH="/usr/local/anaconda3/bin:$PATH"
Now we can create a conda environment for the PLUMED Masterclass:
conda create --name plumed-masterclass-2022
and activate it with:
conda activate plumed-masterclass-2022
Finally, we can proceed with the installation of the required software:
# install some basic analysis tool and the default plumed version
conda install -c conda-forge plumed py-plumed numpy pandas matplotlib notebook mdtraj mdanalysis git
# install plumed 2.7.3 and gromacs 2020.6 with MPI and all modules enabled
conda install --strict-channel-priority -c plumed/label/masterclass-2022 -c conda-forge plumed gromacs
Conda will install a number of packages. On MacOS, for instance, you should see something similar to this:
boost-cpp conda-forge/osx-64::boost-cpp-1.77.0-hf3dc895_1
bzip2 conda-forge/osx-64::bzip2-1.0.8-h0d85af4_4
fftw conda-forge/osx-64::fftw-3.3.10-nompi_hf082fe4_102
gawk conda-forge/osx-64::gawk-5.1.0-h8a989fb_0
gettext conda-forge/osx-64::gettext-0.19.8.1-hd1a6beb_1008
gromacs plumed/label/masterclass-2022/osx-64::gromacs-2020.6-h75233e6_0
gsl conda-forge/osx-64::gsl-2.7-h93259b0_0
icu conda-forge/osx-64::icu-69.1-he49afe7_0
libblas conda-forge/osx-64::libblas-3.9.0-13_osx64_openblas
libcblas conda-forge/osx-64::libcblas-3.9.0-13_osx64_openblas
libcxx conda-forge/osx-64::libcxx-12.0.1-habf9029_1
libffi conda-forge/osx-64::libffi-3.4.2-h0d85af4_5
libgfortran conda-forge/osx-64::libgfortran-5.0.0-9_3_0_h6c81a4c_23
libgfortran5 conda-forge/osx-64::libgfortran5-9.3.0-h6c81a4c_23
libhwloc conda-forge/osx-64::libhwloc-1.11.13-hc10311c_0
libiconv conda-forge/osx-64::libiconv-1.16-haf1e3a3_0
liblapack conda-forge/osx-64::liblapack-3.9.0-13_osx64_openblas
libopenblas conda-forge/osx-64::libopenblas-0.3.18-openmp_h3351f45_0
libxml2 conda-forge/osx-64::libxml2-2.9.12-h7e28ab6_1
libzlib conda-forge/osx-64::libzlib-1.2.11-h9173be1_1013
llvm-openmp conda-forge/osx-64::llvm-openmp-12.0.1-hda6cdc1_1
lz4-c conda-forge/osx-64::lz4-c-1.9.3-he49afe7_1
mpi conda-forge/osx-64::mpi-1.0-openmpi
ncurses conda-forge/osx-64::ncurses-6.3-he49afe7_0
openmpi conda-forge/osx-64::openmpi-4.1.2-hd3cd54c_0
plumed plumed/label/masterclass-2022/osx-64::plumed-2.7.3-h75233e6_0
readline conda-forge/osx-64::readline-8.1-h05e3726_0
xdrfile conda-forge/osx-64::xdrfile-1.1.4-h0d85af4_1
xz conda-forge/osx-64::xz-5.2.5-haf1e3a3_1
zlib conda-forge/osx-64::zlib-1.2.11-h9173be1_1013
zstd conda-forge/osx-64::zstd-1.5.2-h582d3a0_0
Make sure that gromacs and plumed packages are installed from plumed/label/masterclass-2022.
Do not forget to activate the plumed-masterclass-2022 environment every time you open a new terminal/shell.