Step 2 / 2_AutomateGromacs.py

Equilibration and Production MD

Runs energy minimization, NVT equilibration, NPT equilibration, and production molecular dynamics with configurable MDP files and CPU/GPU resource controls.

Why this step matters

The prepared system must relax, reach the target temperature, reach the target pressure and density, and only then produce a trajectory suitable for interpretation.

Concepts to understand

steepest-descents energy minimization NVT temperature equilibration NPT pressure and density equilibration production trajectory generation checkpoint-aware restart behavior CPU, GPU, thread, MPI, and index-group control

Before production MD

Step 2 runs three stabilization stages before production trajectory collection. Open each page to learn what it does, what files it reads and writes, and what to check before moving forward.

EM Energy Minimization Energy minimization relaxes severe steric clashes and unfavorable contacts before atoms are allowed to move with real velocities. NVT NVT Equilibration NVT equilibration brings the minimized system to the target temperature while keeping the box volume fixed. NPT NPT Equilibration NPT equilibration lets the box volume adjust so pressure, density, solvent packing, and the restrained solute environment become production-ready.

Common outputs

em.gro nvt.tpr npt.tpr md_0_1.tpr md_0_1.xtc md_0_1.edr md_0_1.cpt mdrun.log

Typical commands

python 2_AutomateGromacs.py

python 2_AutomateGromacs.py --compute GPU --gpu-id 0 --ntomp 8 --ntmpi 1

python 2_AutomateGromacs.py --equilibration-plan docs/equilibration_plan_example.json