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Run GROMACS molecular dynamics simulations on Deadline Cloud - Deadline Cloud

Run GROMACS molecular dynamics simulations on Deadline Cloud

The gromacs_md job bundle runs a GROMACS molecular dynamics simulation pipeline from raw protein structure to analyzed trajectory. The pipeline runs system preparation, energy minimization, NVT/NPT equilibration, production MD, and analysis (RMSD, RMSF, radius of gyration, hydrogen bonds). Multiple independent replicas fan out in parallel through the MaxReplicaIndex parameter.

The bundle requires a Deadline Cloud farm with a Linux x86_64 service-managed fleet (minimum 4 vCPU) and a conda queue environment with gromacs from conda-forge. No host configuration script or custom conda recipe is needed.

The bundle includes sample data for hen egg-white lysozyme (PDB: 1AKI) and MDP parameter files under sample_inputs/mdp/.

From the job_bundles directory, submit the job:

deadline bundle submit gromacs_md \
  -p "InputPdb=sample_inputs/protein.pdb" \
  -p "MdpMinimization=sample_inputs/mdp/minimization.mdp" \
  -p "MdpNvt=sample_inputs/mdp/nvt.mdp" \
  -p "MdpNpt=sample_inputs/mdp/npt.mdp" \
  -p "MdpProduction=sample_inputs/mdp/production.mdp" \
  -p "ProductionSteps=500000"

To run 10 independent replicas in parallel:

deadline bundle submit gromacs_md \
  -p "InputPdb=protein.pdb" \
  -p "MaxReplicaIndex=9" \
  -p "ProductionSteps=5000000"