xBFreE Installation¶

Currently, xBFreE can be installed using three ways:

• Manual installation
• Docker Package (coming soon!)
• Singularity Package (coming soon!)

Manual installation¶

You can carry out the installation of xBFreE in three ways:

conda environment (Recommended for PC installation)

The conda environment provides a clean and efficient way of installing xBFreE. It also allows to have different versions of xBFreE in isolated environments, thus reducing the possibility of incompatibility with other packages. Installation time is also less since it does not require the compilation of AmberTools or GROMACS.

$ curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
---> 100%

$ chmod +x Miniconda3-latest-Linux-x86_64.sh

$ ./Miniconda3-latest-Linux-x86_64.sh
---> 100%

Successful miniconda intallation

curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh   # (1)!
chmod +x Miniconda3-latest-Linux-x86_64.sh                                      # (2)!
./Miniconda3-latest-Linux-x86_64.sh                                             # (3)!

virtual environment (Recommended for HPC installation -- coming soon!)

The virtual environment provides a clean and efficient way of installing xBFreE. It also allows to have different versions of xBFreE in isolated environment, thus reducing the possibility of incompatibility with other packages. Differently to conda environment this environment only contain python packages and not pre-compiled libraries.

AmberTools compilation (Recommended when you need to modify sander o compile AmberTools in a specific way)

In this way, we assume that you have AmberTools compiled on your machine and that you want to do an installation without worrying about enabling or disabling conda environments. It also involves user compilation of GROMACS, which takes considerable installation time. This way also requires installed packages to be compatible and installation errors are more frequent.

Preparing the environment¶

Before installing xBFreE we need to prepare the environment with all dependencies.

// Create a new environment and use the *.yml file to install dependencies
$ conda env create -n xbfree-env --file env.yml

// To use xBFreE, just activate the environment
$ conda activate xbfree-env

conda env create -n xbfree-env --file env.yml                                    # (1)!
conda activate xbfree-env                                                        # (2)!

// Update conda
$ conda update conda

// Create a new environment and activate it
$ conda create -n xbfree-env python=3.9 -y -q 
$ conda activate xbfree-env

// Install mpi4py and AmberTools
$ conda install -c conda-forge mpi4py=3.1.3 ambertools=21.12 compilers=1.2.0 -y -q

// Install updated version of ParmEd
$ python -m pip install git+https://github.com/Valdes-Tresanco-MS/ParmEd.git@v3.4

// Install PyQt5 required to use the GUI analyzer tool (xBFreE-Analyzer). Not needed for HPC
$ python -m pip install pyqt5

// (Optional) Install GROMACS
$ conda install -c conda-forge gromacs==2022.4 -y -q

// Install the latest version available in PYPI and xBFreE-Analyzer
$ python -m pip install xbfree[xbfree-analyzer]

conda update conda
conda create -n xbfree-env python=3.9 -y -q                                      # (1)
conda activate xbfree-env                                                        # (2)
conda install -c conda-forge mpi4py=3.1.3 ambertools=21.12 compilers=1.2.0 -y -q      # (3)
python -m pip install git+https://github.com/Valdes-Tresanco-MS/ParmEd.git@v3.4 # (4)
python -m pip install pyqt5                                                     # (5)
# Optional
conda install -c conda-forge gromacs==2022.4 -y -q                                 # (6)

// Install uodated ParmEd
$ amber.python -m pip install git+https://github.com/Valdes-Tresanco-MS/ParmEd.git@v3.4
// Install xBFreE
$ amber.python -m pip install xBFreE                                               

// Update xBFreE
$ amber.python -m pip install xBFreE -U

// Install updated ParmEd
$ amber.python -m pip install git+https://github.com/Valdes-Tresanco-MS/ParmEd.git@v3.4
// Install xBFreE
$ amber.python -m pip install git+https://github.com/Valdes-Tresanco-MS/xBFreE     

amber.python -m pip install git+https://github.com/Valdes-Tresanco-MS/xBFreE -U

amber.conda install -c conda-forge mpi4py=3.1.3

amber.conda install pip

Installing xBFreE¶

The steps described below includes the installation of the latest xBFreE release. Here, we show you how install/update other versions from PYPI or directly from the GitHub Repository

// INSTALLATION
$ python -m pip install xBFreE

// UPDATE
$ python -m pip install xBFreE -U

// INSTALLATION
$ python -m pip install git+https://github.com/xBFreEnergy/xBFreE.git

// UPDATE
$ python -m pip install git+https://github.com/xBFreEnergy/xBFreE.git -U

Docker Package¶

Coming soon! sds

Singularity Package¶

Coming soon!

Testing the operation of xBFreE¶

After preparing everything to run xBFreE, it only remains to check its correct operation. To know how to do it, consult the documentation of xBFreE_test