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Compiling Gromacs with CP2K for QMMM simulation

Jun 15, 2025, 4 min read

Hybrid Quantum-Classical simulations (QM/MM) with CP2K interface

In a molecular mechanics (MM) force field, the influence of electrons is expressed by empirical parameters that are assigned on the basis of experimental data, or on the basis of results from high-level quantum chemistry calculations. These are valid for the ground state of a given covalent structure, and the MM approximation is usually sufficiently accurate for ground-state processes in which the overall connectivity between the atoms in the system remains unchanged. However, for processes in which the connectivity does change, such as chemical reactions, or processes that involve multiple electronic states, such as photochemical conversions, electrons can no longer be ignored, and a quantum mechanical description is required for at least those parts of the system in which the reaction takes place. One approach to the simulation of chemical reactions in solution, or in enzymes, is to use a combination of quantum mechanics (QM) and molecular mechanics (MM). The reacting parts of the system are treated quantum mechanically, with the remainder being modeled using the force field. The current version of GROMACS provides an interface to the popular Quantum Chemistry package CP2K 1

Preparing CP2K interface for QM part

Integrating the CP2K QM/MM interface into GROMACS will require linking against the libcp2k library, which incorporates CP2K functionality.

Notice

CP2K version 8.1 or higher and Gromacs version 2022 or higher are requred. Here I used CP2K 2024.1 and Gromacs 2024.2.

Dependencies preparation

OpenMPI

Although CP2K can automatically install OpenMPI, I opted to compile it manually to ensure compatibility with the specific OpenMPI version required by other software.

wget https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.1.tar.bz2
tar -xvf openmpi-4.1.1.tar.bz2
cd openmpi-4.1.1/
./configure --prefix=/opt/openmpi411 --disable-builtin-atomics
sudo make -j 12 install

Note that the installation directory, such as /opt/openmpi411, can be located anywhere you prefer.

After installation, add openmpi library into PATH by editting ~/.bashrc :

export PATH=/opt/openmpi411/bin:$PATH
export LD_LIBRARY_PATH=/opt/openmpi411/lib:$LD_LIBRARY_PATH

Note that after each time you edit the .bashrc file, don’t forget to apply the changes:

source ~/.bashrc

FFTW

If your CPUs support AVX2, it is recommended to compile the fftw library yourself using the --enable-avx2 option to accelerate the simulation process.

wget http://www.fftw.org/fftw-3.3.10.tar.gz
tar -zxf fftw-3.3.10.tar.gz
cd fftw-3.3.10/
./configure --prefix=/opt/fftw3310 --enable-mpi --enable-openmp --enable-sse2 --enable-avx --enable-float --enable-shared --enable-avx2
sudo make -j 12 install

Similarly, the installation directory /opt/fftw3310 can be located anywhere you prefer.

After installation, add fftw library into PATH by editting ~/.bashrc :

export PATH=/opt/fftw3310/bin:$PATH
export LD_LIBRARY_PATH=/opt/fftw3310/lib:$LD_LIBRARY_PATH

Compiling CP2K

Here, I use CP2K version 2024.1. The components used for compiling CP2K should be compatible with those of Gromacs.

Install CP2K with toolchain:

cd /path/to/cp2k/
cd tools/toolchain/
./install_cp2k_toolchain.sh \
--with-libxsmm=install \
--with-elpa=install \
--with-libxc=install \
--with-libint=install \
--with-gsl=no \
--with-libvdwxc=no \
--with-spglib=no \
--with-hdf5=no \
--with-spfft=no \
--with-cosma=no \
--with-libvori=no \
--with-sirius=no \
--with-scalapack=install \
--with-openblas=install \
--with-fftw=/opt/fftw3310 \
--with-openmpi=system \
--with-plumed=install

This process will take tens of minutes. You can also utilize previously installed components in your system, such as by specifying --with-openblas=system.

Note that the location of FFTW (/opt/fftw3310, or other location you specified when installing FFTW) must be specified; otherwise, errors will occur during the compilation of Gromacs.

After this process, all components installed by toolchain can be found in /path/to/cp2k/tools/toolchain/install/.

Then we can complie CP2K:

cp install/arch/* ../../arch/
source install/setup
make -j 12 ARCH=local VERSION="ssmp psmp"
make -j 12 ARCH=local VERSION="ssmp psmp" libcp2k

If the compilation succeeds, you should find the executable files in /path/to/cp2k/exe/, and the libcp2k.a file in /path/to/cp2k/lib/psmp/.

Add CP2K into PATH by editting ~/.bashrc:

source /path/to/cp2k/tools/toolchain/install/setup
export PATH=$PATH:/path/to/cp2k/exe/local
export CP2K_DATA_DIR=/path/to/cp2k/data

Compiling Gromacs

Here, I use Gromacs version 2024.2. The compilation process for Gromacs is much simpler than that for CP2K, as most of the dependencies have already been prepared during the CP2K compilation.

cd /path/to/gromacs
mkdir build
cd build/
cmake .. -DCMAKE_PREFIX_PATH=/opt/fftw3310 \
-DCMAKE_INSTALL_PREFIX=/path/to/gromacs/ \
-DBUILD_SHARED_LIBS=OFF \
-DGMXAPI=OFF \
-DGMX_INSTALL_NBLIB_API=OFF \
-DGMX_DOUBLE=ON \
-DGMX_MPI=ON \
-DGMX_FFT_LIBRARY=fftw3 \
-DGMX_BLAS_USER=/path/to/cp2k/tools/toolchain/install/openblas-0.3.25/lib/libopenblas.so \
-DGMX_LAPACK_USER=/path/to/cp2k/tools/toolchain/install/openblas-0.3.25/lib/libopenblas.so \
-DGMX_CP2K=ON \
-DCP2K_DIR=/path/to/cp2k/lib/local/psmp \
-DGMX_DEFAULT_SUFFIX=OFF \
-DCP2K_LINKER_FLAGS="..." \
-DMPI_C_COMPILER=/opt/openmpi411/bin/mpicc \
-DMPI_C_COMPILER=/opt/openmpi411/bin/mpicxx \
-DMPI_Fortran_COMPILER=/opt/openmpi411/bin/mpif90

-DGMX_BLAS_USER and -DGMX_LAPACK_USER options specify the library for BLAS and LAPACK, which are provided by libopenblas.

-DCP2K_LINKER_FLAGS option specifies libraries which should be compatible with those used for the compilation of CP2K. Specifically, you can find them in the /path/to/cp2k/tools/toolchain/install/arch/local.psmp file:

LDFLAGS     =  $(FCFLAGS) ...
LIBS        = ...

-DMPI_C_COMPILER, -DMPI_C_COMPILER and -DMPI_Fortran_COMPILER specify comilers used for compilation. You should specify them if there’re multiple compilers for MPI compiling in your machine.

Compile Gromacs:

make -j 12
sudo make -j 12 install

You should find the executable files in /path/to/gromacs/bin if the compilation succeeds.

Add Gromacs into ~/.bashrc:

source /path/to/gromacs/bin/GMXRC
export PATH=$PATH:/path/to/gromacs/bin
Just enjoy QM/MM simulation with Gromacs and CP2K!

Footnotes

  1. See Gromacs Manual “Hybrid Quantum-Classical simulations (QM/MM) with CP2K interface” ↩

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