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Install GROMACS with DeepMD

Patch source code of GROMACS

Download 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

where deepmd_kit_root is the directory where the latest version of deepmd-kit is installed, and gromacs_root refers to source code directory of gromacs. And version represents the version of gromacs, only support 2020.2 now. You may patch another version of gromacs but still setting version to 2020.2. However, we cannot ensure that it works.

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 scipt:

#!/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