https://github.com/plumed/conda
Repository with conda recipes for LAMMPS, GROMACS, etc (WIP)
https://github.com/plumed/conda
Last synced: about 2 months ago
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Repository with conda recipes for LAMMPS, GROMACS, etc (WIP)
- Host: GitHub
- URL: https://github.com/plumed/conda
- Owner: plumed
- Created: 2019-07-03T15:35:23.000Z (almost 6 years ago)
- Default Branch: master
- Last Pushed: 2024-04-11T19:55:49.000Z (about 1 year ago)
- Last Synced: 2025-04-17T22:09:25.495Z (about 2 months ago)
- Language: Shell
- Size: 338 KB
- Stars: 10
- Watchers: 2
- Forks: 10
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# 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
````