envs/abmelt_md_simulation_env/linux_cuda_machine_setup.md

tested on machine RTX 2000 Ada runpod

• apt install gromacs
• check if in path gmx --version
• use poetry & conda
• conda create -n abmelt-3-11-env python=3.11 -y
• conda activate abmelt-3-11-env
• conda install -c conda-forge openmm pdbfixer -y
• conda install -c bioconda anarci -y
• conda install -c conda-forge libgcc-ng libstdcxx-ng
• poetry install
• python quick_test.py
• python infer.py --pdb AbMelt/public_tm/train_pdbs/alemtuzumab.pdb --name alemtuzumab.pdb

apt upgrade apt install build-essential cmake libfftw3-dev libopenmpi-dev openmpi-bin

wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-2024.tar.gz tar -xzf gromacs-2024.tar.gz cd gromacs-2024

mkdir build cd build

cmake ..
-DGMX_BUILD_OWN_FFTW=ON
-DGMX_GPU=CUDA
-DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda
-DGMX_CUDA_TARGET_COMPUTE=89
-DCMAKE_INSTALL_PREFIX=/usr/local/gromacs
-DCMAKE_C_COMPILER=gcc
-DCMAKE_CXX_COMPILER=g++
-DGMX_HWLOC=ON
-DGMX_OPENMP=ON

make -j$(nproc) make install

echo 'source /usr/local/gromacs/bin/GMXRC' >> ~/.bashrc source ~/.bashrc

• import gromacs; gromacs.config.setup()