Gromacs

Gromacs is a molecular dynamics software package used to study biomolecular systems. When creating an instance on WebCal and selecting an image, choose the Gromacs image to create an instance equipped with the Gromacs software package. The pre-installed Gromacs has been compiled with CUDA and will use GPU acceleration for computations by default.

The following Gromacs test cases (Source of test cases):

# Step.0: 准备
mkdir test && cd test
wget https://confluence.csuc.cat/download/attachments/29362353/2n6m.pdb

# Step.1: 生成输入文件。这条命令请单独执行，否则会卡住。提示时选择14: GROMOS96 54a7和1:SPC.
gmx pdb2gmx -f 2n6m.pdb -o esculentin.gro -p esculentin.top -ignh

# Step.2: 设置模拟参数
gmx editconf -f esculentin.gro -o esculenbox.gro -box 5 5 5
gmx solvate -cp esculenbox.gro -o solvated.gro -p esculentin.top

# Step.3: 配置
cat > options.mdp << EOF
integrator        = md
nsteps            = 50000000
nstxout            = 50000
coulombtype        = PME
fourierspacing    = 0.15
tcoupl            = v-rescale
tau-t            = 0.2 0.2
ref-t            = 298.15 298.15
tc-grps            = Protein Non-protein
pcoupl            = berendsen
compressibility    = 4.5e-5
tau-p            = 0.2
ref-p            = 1.0
EOF
gmx grompp -f options.mdp -c solvated.gro -p esculentin.top -o esculentin.tpr -maxwarn 100

# Step.4: 运行
gmx mdrun -s esculentin.tpr

Attached is the Gromacs installation script:

wget https://ftp.gromacs.org/gromacs/gromacs-2022.2.tar.gz \
    && tar xfz gromacs-2022.2.tar.gz \
    && cd gromacs-2022.2 \
    && mkdir build \
    && cd build \
    && /root/miniconda3/bin/cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=CUDA -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda \
    && make -j8 && make check && make install \
    && cd ../../ && rm -rf gromacs-* \
    && echo "PATH=/usr/local/gromacs/bin/:\$PATH" >> /etc/profile

If you are compiling Gromacs version 2022 yourself, please be sure not to use CUDA 11.3. See the official explanation.

The following Gromacs test cases (Source of test cases):

# Step.0: 准备
mkdir test && cd test
wget https://confluence.csuc.cat/download/attachments/29362353/2n6m.pdb

# Step.1: 生成输入文件。这条命令请单独执行，否则会卡住。提示时选择14: GROMOS96 54a7和1:SPC.
gmx pdb2gmx -f 2n6m.pdb -o esculentin.gro -p esculentin.top -ignh

# Step.2: 设置模拟参数
gmx editconf -f esculentin.gro -o esculenbox.gro -box 5 5 5
gmx solvate -cp esculenbox.gro -o solvated.gro -p esculentin.top

# Step.3: 配置
cat > options.mdp << EOF
integrator        = md
nsteps            = 50000000
nstxout            = 50000
coulombtype        = PME
fourierspacing    = 0.15
tcoupl            = v-rescale
tau-t            = 0.2 0.2
ref-t            = 298.15 298.15
tc-grps            = Protein Non-protein
pcoupl            = berendsen
compressibility    = 4.5e-5
tau-p            = 0.2
ref-p            = 1.0
EOF
gmx grompp -f options.mdp -c solvated.gro -p esculentin.top -o esculentin.tpr -maxwarn 100

# Step.4: 运行
gmx mdrun -s esculentin.tpr

Attached is the Gromacs installation script:

wget https://ftp.gromacs.org/gromacs/gromacs-2022.2.tar.gz \
    && tar xfz gromacs-2022.2.tar.gz \
    && cd gromacs-2022.2 \
    && mkdir build \
    && cd build \
    && /root/miniconda3/bin/cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=CUDA -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda \
    && make -j8 && make check && make install \
    && cd ../../ && rm -rf gromacs-* \
    && echo "PATH=/usr/local/gromacs/bin/:\$PATH" >> /etc/profile

If you are compiling Gromacs version 2022 yourself, please be sure not to use CUDA 11.3. See the official explanation.