1.6. Install GROMACS with DeepMD
Before following this section, DeePMD-kit C++ interface should have be installed.
1.6.1. Patch source code of GROMACS
Download the source code of a supported GROMACS version (2020.2) from https://manual.gromacs.org/2020.2/download.html. Run the following command:
export PATH=$PATH:$deepmd_kit_root/bin dp_gmx_patch -d $gromacs_root -v $version -p
deepmd_kit_root is the directory where the latest version of DeePMD-kit is installed, and
gromacs_root refers to the source code directory of GROMACS. And
version represents the version of GROMACS, where only 2020.2 is supported now. If attempting to patch another version of GROMACS you will still need to set
2020.2 as this is the only supported version, we cannot guarantee that patching other versions of GROMACS will work.
1.6.2. Compile GROMACS with deepmd-kit
The C++ interface of
Deepmd-kit 2.x and
TensorFlow 2.x are required. And be aware that only DeePMD-kit with high precision is supported now since we cannot ensure single precision is enough for a GROMACS simulation. Here is a sample compile script:
#!/bin/bash export CC=/usr/bin/gcc export CXX=/usr/bin/g++ export CMAKE_PREFIX_PATH="/path/to/fftw-3.3.9" # fftw libraries mkdir build cd build cmake3 .. -DCMAKE_CXX_STANDARD=14 \ # not required, but c++14 seems to be more compatible with higher version of tensorflow -DGMX_MPI=ON \ -DGMX_GPU=CUDA \ # Gromacs on ROCm has not been fully developed yet -DCUDA_TOOLKIT_ROOT_DIR=/path/to/cuda \ -DCMAKE_INSTALL_PREFIX=/path/to/gromacs-2020.2-deepmd make -j make install