Scripts¶
MDP Templates¶
The GROMACS MDP templates live in the repository under scripts/gromacs/mdps/.
They are organized by force field:
# CHARMM-style templates
cp scripts/gromacs/mdps/charmm/*.mdp ./my_simulation/
# AMBER-style templates
cp scripts/gromacs/mdps/amber/*.mdp ./my_simulation/
Available Templates¶
Five standard GROMACS simulation stages:
| File | Stage |
|---|---|
step4.0_minimization.mdp |
Energy minimization |
step4.1_equilibration.mdp |
NVT equilibration |
step4.2_equilibration.mdp |
NPT equilibration |
step4.3_equilibration.mdp |
Final equilibration |
step5_production.mdp |
Production MD |
Scripts¶
All shell scripts live in the top-level scripts/ directory and are not included in
the pip-installed package. Copy or symlink them into your MD working directories as
needed.
GROMACS¶
Analysis (scripts/gromacs/analysis/)¶
| Script | Description |
|---|---|
gmx_rmsd.sh |
RMSD calculation |
gmx_rmsf.sh |
RMSF calculation |
gmx_dssp.sh |
Secondary structure (DSSP) |
gmx_hbond.sh |
Hydrogen bond analysis |
gmx_energy.sh |
Energy analysis |
gmx_gyrate.sh |
Radius of gyration |
gmx_sasa.sh |
Solvent accessible surface area |
gmx_cluster.sh |
Conformational clustering |
Runtime (scripts/gromacs/runtime/)¶
| Script | Description |
|---|---|
check_status.sh |
Monitor simulation job status |
restart.sh |
Restart from checkpoint |
extend.sh |
Extend simulation time |
export.sh |
Export trajectory |
MD Run (scripts/gromacs/mdrun/)¶
| Script | Description |
|---|---|
mdprep.sh |
Minimization & equilibration pipeline |
mdrun.sh |
Production run (GPU-accelerated) |
rest2/rest2.sh |
REST2 topology setup |
rest2/mdrun_mpi_plumed.sh |
REST2 with PLUMED (multi-replica) |
Other Categories¶
scripts/gromacs/mdps/-- force-field-specific MDP templatesscripts/gromacs/compilation/-- GROMACS build scripts (generic + Sherlock HPC)scripts/gromacs/mdenv/-- Environment setup scripts (Sherlock)scripts/gromacs/data_transfer/-- DTN download scripts (Sherlock)scripts/gromacs/postprocessing/-- Trajectory postprocessingscripts/gromacs/visualization/-- PyMOL movie generation
SLURM (Sherlock HPC)¶
SLURM batch scripts (.sbatch) live alongside their .sh counterparts in each category directory.
OpenFE¶
Requires OpenFE >= 1.10.0 for checkpoint-based resumption (--resume).
| Script | Description |
|---|---|
quickrun/quickrun.sh |
Submit all transformations/*.json as SLURM array jobs |
quickrun/quickrun.sbatch |
SLURM batch script: starts CUDA MPS, runs openfe quickrun --resume via Apptainer |
runtime/check_status.sh |
Check transformation replica status and optionally restart failed replicas |
runtime/monitor.sbatch |
Periodic monitor: runs check_status, emails report, self-resubmits via SLURM |
Quick start¶
# Copy scripts to your working directory (alongside transformations/)
cp -r scripts/openfe/{quickrun,runtime} /path/to/workdir/
cd /path/to/workdir/
# Submit with 3 independent repeats per transformation
./quickrun/quickrun.sh -r 3
# Check status of all transformations
./runtime/check_status.sh
# Start periodic monitoring (emails reports, restarts failures, self-resubmits)
sbatch runtime/monitor.sbatch -d /path/to/workdir -e $USER@stanford.edu
Output structure¶
results/<transformation_name>/replica_0/
results/<transformation_name>/replica_1/
results/<transformation_name>/replica_2/
Preemption handling¶
Jobs on the owners partition are automatically requeued when preempted.
quickrun.sbatch uses --resume so requeued jobs continue from the last
checkpoint instead of starting over. CUDA MPS is started automatically to
work around Sherlock's Exclusive_Process GPU mode.