OpenMM MD framework

Small workflow for running OpenMM simulations starting from Amber prmtop and inpcrd/rst7 files.

The workflow has three scripts:

Script	Purpose
openmm_prep.py	Builds system.xml, optionally adds Amber-mask positional restraints, minimizes, and writes sys_min.xml.
openmm_md.py	Runs one MD stage from system.xml plus an input state, writing a new restart/state XML, DCD, log, and checkpoint.
openmm_generate_script.py	Generates a resumable run_simulation.sh for minimization, NVT, NPT, and segmented production MD.

Requirements

Install in a clean conda/mamba environment:

mamba create -n openmm-md -c conda-forge python=3.11 openmm parmed mdtraj ambertools
mamba activate openmm-md

parmed is required only if you use Amber-mask restraints such as !:WAT&!@H=.

Quick start

From a directory containing complex_solvated.prmtop, complex_solvated.inpcrd, and a reference PDB with matching atom order:

python openmm_generate_script.py \
  -i complex_solvated.inpcrd \
  -t complex_solvated.prmtop \
  --reference prot_amber.pdb \
  --restrain-mask '!:WAT&!@H=' \
  minim nvt npt md

bash run_simulation.sh

Default times are:

• NVT: 1 ns
• NPT: 2 ns
• Production: 10 ns split into 5 segments
• timestep: 2 fs
• temperature: 298.15 K
• Langevin friction: 1 ps⁻¹

Longer production example

python openmm_generate_script.py \
  -i complex_solvated.inpcrd \
  -t complex_solvated.prmtop \
  --reference prot_amber.pdb \
  --restrain-mask '!:WAT&!@H=' \
  minim nvt npt md \
  --nvt-time 2 \
  --npt-time 5 \
  --md-time 100 \
  --prod-segments 20 \
  --dt 2.0 \
  --temp 310 \
  --platform CUDA --cuda 0

bash run_simulation.sh

Running stages manually

1. Prepare and minimize

python openmm_prep.py \
  -t complex_solvated.prmtop \
  -i complex_solvated.inpcrd \
  --system-xml system.xml \
  --min-state sys_min.xml \
  --longrange PME \
  --cutoff 10.0 \
  --shake \
  --restrain-mask '!:WAT&!@H=' \
  --reference prot_amber.pdb \
  -k 10.0

2. NVT

python openmm_md.py \
  --xml system.xml \
  -t complex_solvated.prmtop \
  -i complex_solvated.inpcrd \
  -s sys_min.xml \
  --restart sys_NVT.xml \
  -x sys_NVT.dcd \
  -r sys_NVT.log \
  --chk sys_NVT.chk \
  --temp 298.15 \
  --gamma-ln 1.0 \
  --dt 2.0 \
  -n 500000

3. NPT

python openmm_md.py \
  --xml system.xml \
  -t complex_solvated.prmtop \
  -s sys_NVT.xml \
  --restart sys_NPT.xml \
  -x sys_NPT.dcd \
  -r sys_NPT.log \
  --chk sys_NPT.chk \
  --npt --pressure 1.0

4. Production segment

python openmm_md.py \
  --xml system.xml \
  -t complex_solvated.prmtop \
  -s sys_NPT.xml \
  --restart sys_md_1.xml \
  -x sys_md_1.dcd \
  -r sys_md_1.log \
  --chk sys_md_1.chk \
  --npt \
  -n 1000000

Notes and conventions

• system.xml stores the force-field system definition. It is reused for all stages.
• sys_min.xml, sys_NVT.xml, sys_NPT.xml, and sys_md_*.xml are serialized OpenMM State files and are used as restart files.
• The generated run_simulation.sh is resumable: a stage is skipped if its target restart XML already exists.
• Positional restraints are currently added in openmm_prep_clean.py, so they become part of system.xml. This means the same restrained system is used in later stages. For unrestrained production, generate a second unrestrained system.xml or extend the scripts to scale/remove the restraint force after equilibration.
• The reference file used for restraints must have the same atom order as the Amber topology.