Get Started with Gromacs
GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions many groups are also using it for research on non-biological systems.
Some test cases to start with can be found at ftp://ftp.gromacs.org/pub/benchmarks/gmxbench-3.0.tar.gz.
Refereneces
Build and Install Gromacs
Download the source code
wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-2020.2.tar.gz |
Build Gromacs for CPU only
tar xfz gromacs-2020.2.tar.gz
cd gromacs-2020.2
module load intel/2019.5.281
module load mkl/2019.5.281
module load gcc/8.4.0
module load cmake/3.13.4
module load hpcx/2.6.0
mkdir build install run
cd build
cmake .. -DGMX_FFT_LIBRARY=mkl -DMKL_LIBRARIES=-mkl \
-DMKL_INCLUDE_DIR=$MKLROOT/include \
-DGMX_SIMD=AVX2_256 \
-DGMX_MPI=ON \
-DGMX_BUILD_MDRUN_ONLY=on \
-DBUILD_SHARED_LIBS=on \
-DGMX_HWLOC=off \
-DCMAKE_INSTALL_PREFIX=../install \
-DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx
make -j 16 install |
Check the install directory for the file mdrun_mpi
$ ls ../install/
bin include lib64 share
$ ls ../install/bin
gmx-completion-mdrun_mpi.bash mdrun_mpi
Build Gromacs with GPU support
Run Gromacs
To run Gromacs with CPU only using stmv case
To run Gromacs with GPU