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
If the Masterclass requires Gromacs, you can then run the following command:
# install plumed 2.8.0 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
If the Masterclass requires LAMMPS instead (for instance, Masterclass 22.12), the appropriate command is:
# install plumed 2.8.0 and lammps 23 Jun 2022 with MPI and all modules enabled
conda install --strict-channel-priority -c plumed/label/masterclass-2022 -c conda-forge plumed lammps
If the Masterclass requires AMBER (for instance, Masterclass 22.13), you should first create a separate AMBER environment:
# create a separate AMBER environment and install AMBER
conda create --name plumed-masterclass-2022-amber
conda activate plumed-masterclass-2022-amber
conda install -c conda-forge ambertools
And you should then stack the PLUMED and AMBER environments:
# stack the PLUMED and AMBER environments
conda activate plumed-masterclass-2022
conda activate --stack plumed-masterclass-2022-amber
export PLUMED_KERNEL=/your_path_here/plumed-masterclass-2022/lib/libplumedKernel.so
Conda will install a number of packages. On MacOS, for instance, you should see something similar to this:
The following NEW packages will be INSTALLED:
boost-cpp conda-forge/osx-64::boost-cpp-1.79.0-h8b082ac_0
gromacs plumed/label/masterclass-2022/osx-64::gromacs-2020.6-h75233e6_1
icu conda-forge/osx-64::icu-70.1-h96cf925_0
libhwloc conda-forge/osx-64::libhwloc-1.11.13-hc10311c_0
libxml2 conda-forge/osx-64::libxml2-2.9.14-h08a9926_0
mpi conda-forge/osx-64::mpi-1.0-openmpi
openmpi conda-forge/osx-64::openmpi-4.1.3-hd33e60e_103
The following packages will be SUPERSEDED by a higher-priority channel:
plumed conda-forge::plumed-2.8.0-nompi_h3651~ --> plumed/label/masterclass-2022::plumed-2.8.0-h75233e6_1
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.
Notice that with some outdated conda version you might receive an error due to the fact that conda confuses python 3.1 with python 3.10. If you find an error like this one:
PackagesNotFoundError: The following packages are not available from current channels:
- python=3.1
Make sure that you have at least conda 4.11.0 (or update conda with conda update conda).
More at this link