xBFreE Installation¶

Currently, xBFreE can be installed using three ways:

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.

Miniconda Installation

Download and install Miniconda

fast →curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
chmod +x Miniconda3-latest-Linux-x86_64.sh
./Miniconda3-latest-Linux-x86_64.sh
Successful miniconda intallation

restart ↻

Copy described intructions

curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh   Download Miniconda installer

chmod +x Miniconda3-latest-Linux-x86_64.sh                                      Change permissions for the installer

./Miniconda3-latest-Linux-x86_64.sh                                             Execute and install miniconda

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.

Require external dependencies

In HPC, the admin recommends using a virtual environment instead of conda to take advantage of optimized compiled programs. In this case, you will require AmberTools, Gromacs, and other dependencies previously compiled (generally as modules)

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.

conda environmentAmberTools compilation

Important

Make sure to have conda installed in your computer.

*.yml filepip

Installing xBFreE using a requierement yml file.

Download env.yml file

fast →💬 Create a new environment and use the *.yml file to install dependenciesconda env create -n xbfree-env --file env.yml
💬 To use xBFreE, just activate the environmentconda activate xbfree-env
restart ↻

Important

The latest release of xBFreE available in PYPI will be installed

Copy described intructions

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

conda activate xbfree-env                                                        Activate xbfree-env environment

Installing dependencies

fast →💬 Update condaconda update conda
💬 Create a new environment and activate itconda create -n xbfree-env python=3.9 -y -qconda activate xbfree-env
💬 Install mpi4py and AmberToolsconda install -c conda-forge mpi4py=3.1.3 ambertools=21.12 compilers=1.2.0 -y -q
💬 Install updated version of ParmEdpython -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 HPCpython -m pip install pyqt5
💬 (Optional) Install GROMACSconda install -c conda-forge gromacs==2022.4 -y -q
💬 Install the latest version available in PYPI and xBFreE-Analyzerpython -m pip install xbfree[xbfree-analyzer]
restart ↻

Copy described intructions

conda update conda
conda create -n xbfree-env python=3.9 -y -q                                      # Create xbfree-env environment

conda activate xbfree-env                                                        # Activate xbfree-env environment

conda install -c conda-forge mpi4py=3.1.3 ambertools=21.12 compilers=1.2.0 -y -q      # Install dependencies

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

python -m pip install pyqt5                                                     # Install PyQt5 if you will use xBFreE-Analyzer

# Optional
conda install -c conda-forge gromacs==2022.4 -y -q                                 # (Optional) Install GROMACS if GROMACS is not installed in your machine

Follow the oficial AmberTools installation according to your OS

Note

We asume that AmberTools and their shell environment are correctly configured

Rolling/stable releasedevelopment version

INSTALLATION

fast →💬 Install uodated ParmEdamber.python -m pip install git+https://github.com/Valdes-Tresanco-MS/ParmEd.git@v3.4💬 Install xBFreEamber.python -m pip install xBFreE
restart ↻

UPDATE

fast →💬 Update xBFreEamber.python -m pip install xBFreE -U
restart ↻

Info

Install xBFreE from PyPI PyPI has the latest version of xBFreE including stable and beta versions.

INSTALLATION

fast →💬 Install updated ParmEdamber.python -m pip install git+https://github.com/Valdes-Tresanco-MS/ParmEd.git@v3.4💬 Install xBFreEamber.python -m pip install git+https://github.com/Valdes-Tresanco-MS/xBFreE
restart ↻

UPDATE

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

restart ↻

Warning

Install/update xBFreE from the master branch of GitHub repository. This version is only recommended to test a new version or to try temporary solutions to reported bugs.

Danger

If you get an error related to installing mpi4py, you may want to install this package manually from conda-forge as follows:

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

If you get an error related to pip, you may want to install this package manually as follows:

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

Rolling/stable releasedevelopment version

INSTALLATION

fast →💬 INSTALLATIONpython -m pip install xBFreE
restart ↻

UPDATE

fast →💬 UPDATEpython -m pip install xBFreE -U
restart ↻

Info

Install/update xBFreE from PyPI. PyPI has the latest version of xBFreE including stable and beta versions.

INSTALLATION

fast →💬 INSTALLATIONpython -m pip install git+https://github.com/xBFreEnergy/xBFreE.git
restart ↻

UPDATE

fast →💬 UPDATEpython -m pip install git+https://github.com/xBFreEnergy/xBFreE.git -U
restart ↻

Warning

Install xBFreE from the master branch of GitHub repository. This is only recommended for testing new versions or temporary solutions to reported bugs.

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

Last update: 1 year ago2023-06-24
Created: 1 year ago2023-06-24