Gromacs

When creating an instance on GPUhuband selecting the image, use the Gromacs image to create an instance that comes with the Gromacs software package pre-installed. The pre-installed Gromacs has been compiled with CUDA, so it will use GPU acceleration for computations by default. Here is a test case for Gromacs (source of the case):

Step 1: Preparation

Create a directory named test and navigate into it.

bash

mkdir test && cd test

Step 2: Generate Input Files

Run this command separately; otherwise, it may hang. When prompted, select 14: GROMOS96 54a7 and 1: SPC.

bash

gmx pdb2gmx -f 2n6m.pdb -o esculentin.gro -p esculentin.top -ignh

Step 3: Set Simulation Parameters

bash

gmx editconf -f esculentin.gro -o esculenbox.gro -box 5 5 5
gmx solvate -cp esculenbox.gro -o solvated.gro -p esculentin.top

Step 4: Configuration

Create a configuration file options.mdp with the following content:

bash

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 5: Run Simulation

bash

gmx mdrun -s esculentin.tpr

Gromacs Installation Script:

bash

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

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Step 1: Preparation

Step 2: Generate Input Files

Step 3: Set Simulation Parameters

Step 4: Configuration

Step 5: Run Simulation

Gromacs Installation Script:

​Step 1: Preparation

​Step 2: Generate Input Files

​Step 3: Set Simulation Parameters

​Step 4: Configuration

​Step 5: Run Simulation

​Gromacs Installation Script:

Step 1: Preparation

Step 2: Generate Input Files

Step 3: Set Simulation Parameters

Step 4: Configuration

Step 5: Run Simulation

Gromacs Installation Script: