OpenMM results depend on more than coordinates and a force field: the force-field, water, and ion files must be compatible; input quantities must use the correct units; and platform, precision, and integrator settings can affect execution and numerical behavior. For reproducible work, record those choices and validate the workflow on the hardware and software stack where it will run. A random seed alone does not guarantee the same trajectory.
How should I pair force-field, water, and ion files?
Treat the XML files used to build a system as a compatibility set, not as interchangeable pieces chosen by similar filenames. OpenMM’s simulation guide demonstrates loading amber19-all.xml with amber19/tip3pfb.xml. In that example, substituting tip3p.xml can produce an exception because the selected solvent definition does not provide the expected ion parameters. This is an example of a specific setup, not a universal recommendation for every molecular system. Check the documentation for the exact force field, water model, and ion parameters you intend to use.
OpenMM User Guide 8.6: Running Simulations
What units does OpenMM use?
OpenMM uses a consistent internal unit system. Convert explicitly when importing values or exchanging data with tools that use conventions such as ångströms, degrees, or kcal/mol.
| Quantity | OpenMM unit |
|---|---|
| Distance | nanometer (nm) |
| Time | picosecond (ps) |
| Mass | atomic mass unit |
| Charge | proton charge |
| Temperature | kelvin (K) |
| Angle | radian |
| Energy | kilojoule per mole (kJ/mol) |
| Force | kilojoule per mole per nanometer (kJ/mol/nm) |
The OpenMM theory guide says its documented physical constants use CODATA 2018 values. OpenMM User Guide 8.6: Introduction
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Which OpenMM platform should I use?
Choose a platform compatible with the hardware available and the purpose of the run. OpenMM documents Reference, CPU, CUDA, HIP, and OpenCL platforms. Reference is intended as clear reference code rather than production speed; CPU targets conventional processors; CUDA targets NVIDIA GPUs; HIP targets ROCm-compatible AMD GPUs; and OpenCL supports a range of GPUs and CPUs. Availability depends on the installed software and device.
OpenMM may choose the fastest available platform by default. You can also select a platform explicitly or use the documented environment variable. Do not interpret automatic selection as a scientific validation: confirm which platform is actually being used and validate the workflow on it.
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OpenMM User Guide 8.6: Platforms
How do precision settings affect a run?
Platform-specific properties include precision choices such as single, mixed, and double, but available options vary by platform. Precision involves a speed-versus-numerical-behavior tradeoff; the documentation does not establish one setting as best for every system or objective. Record the chosen precision and any other platform-specific properties so another run can be compared on like terms.
OpenMM User Guide 8.6: Platform-Specific Properties
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Does the same random seed guarantee the same trajectory?
No. OpenMM documents that different seeds produce different random sequences, but explicitly does not guarantee identical outcomes for identical seeds. Platform algorithms may be nondeterministic, so repeatability can depend on more than the seed, including platform, precision, software version, system construction, and integrator settings. Record seeds as useful metadata, not as a universal reproducibility switch.
The seed guidance is documented for the RPMDIntegrator; do not assume that statement alone specifies every stochastic component or integrator. OpenMM Python API 8.6: RPMDIntegrator
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Can two platforms produce identical results?
They may under particular methods and settings, but identity should not be assumed. Platform implementations can differ in unspecified behavior and numerical precision; the same program may therefore produce meaningfully different results on different platforms. Determinism can depend on the method and precision, and documented behavior may change in future versions.
OpenMM’s theory guide states: “It is essential that you validate your simulation methodology on each Platform you intend to use, and do not assume that good results on one Platform will guarantee good results on another Platform when using identical parameters.” OpenMM User Guide 8.6: Introduction
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How do I make an OpenMM simulation reproducible?
Build a record detailed enough to reconstruct the system and execution environment. OpenMM’s documented seed limits and platform differences make a seed or parameter list on its own insufficient.
- OpenMM version and relevant software environment.
- Topology and coordinate inputs.
- Force-field, water, and ion XML filenames and versions.
- System-building code and choices.
- Integrator class, parameters, and random seeds.
- Selected platform, device, precision, and platform-specific properties.
- Output and checkpoint details needed to identify the run and its state.
Validate the methodology on the intended platform rather than inferring equivalence from results obtained elsewhere. OpenMM provides a guide to testing and validation: OpenMM User Guide 8.6: Testing and Validation.
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