diff --git a/content/notes/compile-gmx-with-cp2k.md b/content/notes/compile-gmx-with-cp2k.md
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+---
+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
+tags:
+  - note/2025/06
+  - note/molecular-dynamics
+id: note20250615184922
+dg-publish: true
+maturity: tree
+---
+> [!quote] 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.
+
+> [!Info] 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.
+
+```bash
+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` :
+``` bash ~/.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:
+```bash
+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.
+
+``` bash
+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, that the installation directory `/opt/fftw3310` can be located anywhere you prefer.
+
+After installation, add `fftw` library into `PATH` by editting `~/.bashrc` :
+``` bash ~/.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`:
+``` bash
+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:
+``` bash
+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`:
+```bash ~/.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.
+
+``` bash
+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`. `libopenblas` provides both of them.
+
+`-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     =  $(FCFLAGS) ...
+LIBS        = ...
+```
+
+`-DMPI_C_COMPILER`, `-DMPI_C_COMPILER` and `-DMPI_Fortran_COMPILER` specify comilers used for compilation. You should specify them if there're multiple compilers for MPI compiling.
+
+Compile Gromacs:
+```bash
+make -j 12
+sudo make -j 12 install
+```
+
+You should find the executable files in `/path/to/gromacs/bin` if the compilation succeeds.
+
+Add Gromacs into `~/.bashrc`:
+```bash
+source /path/to/gromacs/bin/GMXRC
+export PATH=$PATH:/path/to/gromacs/bin
+```
+
+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)"
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diff --git a/content/readings/existentialisme-est-un-humanisme.md b/content/readings/existentialisme-est-un-humanisme.md
index a9f4f84..bec9583 100644
--- a/content/readings/existentialisme-est-un-humanisme.md
+++ b/content/readings/existentialisme-est-un-humanisme.md
@@ -6,7 +6,7 @@ title: 存在主义是一种人道主义
 author: "[法]让-保罗·萨特"
 cover: https://cdn.freezing.cool/images/202403051223853.jpg
 date: 2024-03-05T12:20
-update: 20254-6013-009085T2::2221:53
+update: 2025-06-15T22:35
 douban: https://book.douban.com/subject/10608319/
 dg-publish: true
 maturity: raindrop
diff --git a/content/readings/in-search-of-tashui-village-a-guide.md b/content/readings/in-search-of-tashui-village-a-guide.md
index c180029..29c2c00 100644
--- a/content/readings/in-search-of-tashui-village-a-guide.md
+++ b/content/readings/in-search-of-tashui-village-a-guide.md
@@ -5,7 +5,7 @@ tags:
 author: 沈至
 cover: https://cdn.freezing.cool/images/202402171426515.jpg
 date: 2024-02-14T20:11
-update: 2024-03-098T2:2230:18
+update: 2025-06-15T22:34
 douban: https://book.douban.com/subject/36527880/
 dg-publish: true
 maturity: tree
diff --git a/content/readings/the-blind-assassin.md b/content/readings/the-blind-assassin.md
index a78e01f..49eccd2 100644
--- a/content/readings/the-blind-assassin.md
+++ b/content/readings/the-blind-assassin.md
@@ -5,7 +5,7 @@ tags:
 author: "[加]玛格丽特·阿特伍德"
 cover: https://cdn.freezing.cool/images/202402171426022.jpg
 date: 2024-02-15T22:23
-update: 2024-03-09T32:2T2414:19
+update: 2025-06-15T22:34
 douban: https://book.douban.com/subject/26748179/
 dg-publish: true
 maturity: raindrop
@@ -25,7 +25,7 @@ title: 盲刺客
 
 # After Reading
 
->[!quote]我想从你那里得到什么呢？
+>[!quote] 我想从你那里得到什么呢？
 >不是爱，因为这个要求过分了。不是原谅，因为那不是你能赐予的。或许只是一名听众，只是一个愿意看望我的人。不过，无论你还要做什么，不要美化我；我并不希望做一具装饰过的颅骨。[^1]
 
 [^1]: 摘自玛格丽特·阿特伍德《盲刺客》
\ No newline at end of file
diff --git a/content/readings/the-continuing-silence-of-a-poet.md b/content/readings/the-continuing-silence-of-a-poet.md
index 1610fb3..6c4ea87 100644
--- a/content/readings/the-continuing-silence-of-a-poet.md
+++ b/content/readings/the-continuing-silence-of-a-poet.md
@@ -5,7 +5,7 @@ tags:
 author: "[以色列]亚伯拉罕·耶霍舒亚"
 cover: https://cdn.freezing.cool/images/202402261313962.jpg
 date: 2024-02-26T13:10
-update: 2024-03200022-2422242974T4050:23
+update: 2025-06-15T22:35
 douban: https://book.douban.com/subject/35552618/
 dg-publish: true
 maturity: raindrop