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.

1 Refereneces
2 Build and Install Gromacs
- 2.1 Download the source code
- 2.2 Build Gromacs for CPU only
- 2.3 Build Gromacs with GPU support
- 2.4 Run Gromacs
3 Other command options

Refereneces

http://manual.gromacs.org/documentation/current/install-guide/index.html

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

HPC-Works

Get Started with Gromacs

Refereneces

Build and Install Gromacs

Download the source code

Build Gromacs for CPU only

Build Gromacs with GPU support

Run Gromacs

Other command options