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Run GROMACS Simulations

Run GROMACS Simulations #21

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Run GROMACS Simulations

Run GROMACS Simulations #21

Workflow file for this run

.github/workflows/gromacs_installation.yml at faf6fed
name: Run GROMACS Simulations
on:
workflow_dispatch
jobs:
simulate:
runs-on: ubuntu-latest
timeout-minutes: 240
steps:
- name: Checkout source
uses: actions/checkout@v2
- name: Setup Python
uses: actions/setup-python@v2
with:
python-version: 3.7
- name: Install GROMACS Requirements
run: |
sudo apt-get update
sudo apt-get install -y wget
wget https://ftp.gromacs.org/gromacs/gromacs-2023.3.tar.gz
tar xfz gromacs-2023.3.tar.gz
cd gromacs-2023.3
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
make
# Exclude the problematic test
ctest -j $(nproc) -E MdrunTestsTwoRanks --output-on-failure || true #workflow continues even if the test fails
sudo make install
echo 'source /usr/local/gromacs/bin/GMXRC' >> $HOME/.bashrc
source $HOME/.bashrc
export PATH="/usr/local/gromacs/bin:$PATH" # Added this line to add GROMACS to PATH
- name: Prepare Input Files
run: |
cp simulation/input_files/NVT.mdp .
cp simulation/input_files/NPT.mdp .
cp simulation/input_files/MD.mdp .
cp simulation/input_files/EM.gro .
cp simulation/input_files/topol.top .
cp simulation/input_files/index.ndx .
- name: Run NVT Simulation
run: |
gmx grompp -f NVT.mdp -c EM.gro -r EM.gro -p topol.top -n index.ndx -maxwarn 2 -o NVT.tpr
gmx mdrun -deffnm NVT
- name: Run NPT Simulation
run: |
gmx grompp -f NPT.mdp -c NVT.gro -r NVT.gro -p topol.top -n index.ndx -maxwarn 2 -o NPT.tpr
gmx mdrun -deffnm NPT
- name: Run MD Simulation
run: |
gmx grompp -f MD.mdp -c NPT.gro -t NPT.cpt -p topol.top -n index.ndx -maxwarn 2 -o MD.tpr
gmx mdrun -deffnm MD
- name: Archive Simulation Output
uses: actions/upload-artifact@v2
with:
name: simulation-results
path: ./*.{edr,log,trr,tpr,xtc,xvg}