Using MD Packages

4.5. Using MD Packages#

4.5.1. Anatomy of an MD Simulation Workflow#

4.5.1.1. Initialization#

  • Create initial configuration and parameterize the force field.

  • Tools: packmol, mbuild/Foyer, ambertools, etc.

4.5.1.2. Equilibration#

  • Energy Minimization: Removes overlaps or poor initial configurations to prevent simulation instability.

    • Methods: Steepest Descent, Conjugate Gradient, L-BFGS, FIRE.

  • NVT Ensemble: Brings system to correct temperature.

    • Use aggressive thermostats (e.g., Isokinetic, Berendsen, Langevin).

    • Be cautious if initial velocities are zero (can cause divide-by-zero errors).

  • NPT Ensemble: Brings system to correct density.

    • Barostat usually has a longer time constant than thermostat.

    • Ensure momentum is zeroed when switching from non-conserving thermostats.

  • Simulate for multiple relaxation times to ensure equilibrium.

    • Use transport coefficients to estimate required time.

    • Monitor observables like energy (U), radial distribution function (g®), and density.

4.5.2. Production#

  • Run long enough to gather statistically independent samples of quantities of interest.

  • Trajectory dumping can be disk-intensive—choose frequency wisely.

  • Use checkpointing (saving restart files) to recover from hardware failures.

4.5.3. Post-processing#

  • Write scripts to compute properties, averages, etc., from simulation outputs.

  • Can be done on HPC clusters or downloaded to local machines.

  • Use existing tools and methods when possible—avoid reinventing the wheel.

4.5.4. Tips#

  • Choose the largest time step (Δt) that still ensures accurate integration—test this.

  • Tune hyperparameters for performance using representative simulations.

  • Run multiple simulation copies to improve statistics and estimate errors.

  • Organize files clearly during parameter sweeps. Example structure:

data/ ├── T-1.0/ │ ├── V-20/ │ │ └── input.sh │ ├── V-30/ │ │ └── input.sh ├── T-1.5/ │ ├── V-205/ │ └── V-301/

  • Consider using tools to manage simulation campaigns.

4.5.6. References#

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