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Pull-Request [Digital-Garden-6-15-2025] from Obsidian #151

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Merged
blleng merged 1 commit into from
Jun 15, 2025
Merged

Pull-Request [Digital-Garden-6-15-2025] from Obsidian #151

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12 changes: 7 additions & 5 deletions content/notes/compile-gmx-with-cp2k.md
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
title: Compiling Gromacs with CP2K for QM/MM simulation
description: Recording the process of compiling Gromacs for QM/MM simulation with CP2K
date: 2025-06-15T18:49
update: 2025-06-16T00:01
update: 2025-06-16T00:08
tags:
- note/2025/06
- note/molecular-dynamics
Expand Down Expand Up @@ -55,7 +55,7 @@ cd fftw-3.3.10/
sudo make -j 12 install
```

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

After installation, add `fftw` library into `PATH` by editting `~/.bashrc` :
``` bash ~/.bashrc
Expand Down Expand Up @@ -139,15 +139,15 @@ cmake .. -DCMAKE_PREFIX_PATH=/opt/fftw3310 \
-DMPI_Fortran_COMPILER=/opt/openmpi411/bin/mpif90
```

`-DGMX_BLAS_USER` and `-DGMX_LAPACK_USER` options specify the library for `BLAS` and `LAPACK`. `libopenblas` provides both of them.
`-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.
`-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:
```bash
Expand All @@ -163,6 +163,8 @@ source /path/to/gromacs/bin/GMXRC
export PATH=$PATH:/path/to/gromacs/bin
```

Enjoy QM/MM simulation with Gromacs and CP2K!
```poetry
Just enjoy QM/MM simulation with Gromacs and CP2K!
```

[^1]: See Gromacs Manual "[Hybrid Quantum-Classical simulations (QM/MM) with CP2K interface](https://manual.gromacs.org/current/reference-manual/special/qmmm.html)"