The Tool Desk
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When an OpenMM simulation crashes, produces NaN energy, or becomes physically unstable, first capture the failure and its configuration; then test the starting structure, minimization, timestep, precision, and platform in a controlled order. No single adjustment fixes every case: the cause can depend on the input, model, OpenMM version, and hardware.
1. Record what failed before changing anything
Keep the original coordinates, input files, and any checkpoint untouched. Save a minimal reproducible copy for troubleshooting, along with the complete traceback and the final log lines. Note the first step at which energies or other observables become abnormal. This helps distinguish a trajectory that diverges over time from a process that exits abruptly.
- Record the OpenMM version, operating system, platform, selected device, and precision property.
- Record the integrator class and parameters, force-field and system setup, how the initial structure was prepared, and any thermostat or barostat.
- Log potential energy, kinetic energy, total energy, and temperature often enough to locate when the behavior changes. OpenMM’s
StateDataReportercan also report time, volume, and density. - Keep the failing input and logs together so that each change can be compared against the same starting point.
If the program exits without an OpenMM exception, treat that separately from a run that continues while its observables become unphysical. The OpenMM documentation does not establish a universal diagnosis for hardware-specific process failures; retain the device and runtime details rather than assuming an energy-stability problem.
2. Check the starting structure before tuning dynamics
Run a local energy minimization before equilibration or production, then inspect whether it completes and whether the resulting structure and energies are plausible. OpenMM exposes simulation.minimizeEnergy(); its tolerance and iteration limit can be set. Reaching a user-imposed iteration limit does not, by itself, show that the structure is adequately prepared.
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If minimization does not behave as expected or the initial forces and energies are unusually large, verify the input structure, atom naming, and parameterization using the tools that built the system. Correct the preparation issue and repeat the diagnostic from the prepared structure before concluding that the production integrator is at fault. The specific cause cannot be inferred from a large force alone.
3. Test whether the timestep or integrator is responsible
For fixed-step dynamics, rerun a short diagnostic segment with a smaller timestep and compare the same observables. Change the timestep while holding the rest of the physical model and settings fixed; otherwise it is difficult to tell which change affected the result. Do not assume a timestep that worked elsewhere will be stable for this system or platform.
When you do not know a suitable step size, OpenMM’s application guide describes two variable-timestep options:
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VariableLangevinIntegratorfor constant-temperature dynamics.VariableVerletIntegratorfor constant-energy dynamics.
These integrators adjust the step size to keep estimated integration error below a selected tolerance. A smaller tolerance produces a smaller average step. The tolerance is a tuning parameter, not a guarantee of absolute accuracy; evaluate the trajectory against the needs of the scientific application. Variable-step Verlet is not symplectic, so it is less suitable when long-term precise energy conservation is the primary goal. The guide advises finding the largest tolerance setting that still gives a sufficiently accurate trajectory for the application.
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If instability remains with conservative timestep settings, return to the starting structure, constraints, force-field setup, and platform rather than repeatedly changing unrelated controls.
4. Compare platform and precision under controlled conditions
OpenMM normally selects the fastest available platform. For a useful comparison, record the selected platform or explicitly choose one in code, or set OPENMM_DEFAULT_PLATFORM. Keep the model and integration settings fixed when testing platforms or precision modes.
OpenMM’s theory documentation explains that platform implementations can differ in details such as constraint algorithms and numerical precision. As a result, a timestep that is stable on one platform may be unstable on another. The OpenMM User Guide 8.6 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.” Test the workflow on every platform intended for production.
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| Precision mode | Documented behavior | Useful diagnostic interpretation |
|---|---|---|
| Single | Fastest and least accurate, according to the OpenMM User Guide 8.6 platform-specific documentation. | Compare with another supported mode if numerical sensitivity is suspected. |
| Mixed | Forces are calculated in single precision and integration in double precision; the guide describes better energy conservation than single precision at a slight speed cost. | Can help test whether integration precision is relevant without changing the physical model. |
| Double | Most accurate of the documented modes, but usually slower. | Use as a controlled comparison where supported; a successful run in this mode still needs validation for the intended scientific use. |
Precision options and device properties are platform-specific. Do not interpret a run that succeeds only in one mode as proof that the original input or settings are scientifically valid.
If exact repeatability matters, consult the platform-specific documentation for the DeterministicForces option where supported. Determinism can vary with platform and method, and its behavior may change between OpenMM versions, so verify it for the installed version and target device.
5. Preserve progress and choose the right restart file
Add a CheckpointReporter to save progress periodically during long runs. OpenMM checkpoints can support an exact continuation under compatible conditions, but they are tied to the same hardware and OpenMM version.
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6. Validate a fix on the intended production setup
After a change, run a short segment on the exact platform and precision mode intended for production. Check whether the prior failure recurs and whether the energy, temperature, and other relevant observables behave acceptably for the application. A fix observed on a different platform or with a different precision mode does not establish stability for the production configuration.
If the failure appears to involve the installation or a library defect rather than one particular model, OpenMM’s 8.6 testing and validation guide describes unit tests, realistic-system tests, and direct force comparisons with other programs. These tests show how OpenMM validates code paths; they do not certify an individual user’s input or hardware configuration.
| Test configuration in the OpenMM 8.6 validation guide | Median relative total-force difference versus Reference |
|---|---|
| OpenCL, single precision | 2.53 × 10-6 |
| OpenCL, double precision | 1.44 × 10-7 |
| CUDA, single precision | 2.56 × 10-6 |
| CUDA, double precision | 8.78 × 10-8 |
These are median relative force differences for the documented test systems and metric in the OpenMM User Guide 8.6; the documentation page does not state a publication year. They are not general error bounds for other simulations.
For case-specific help, provide the minimal reproducible input, full traceback, failure logs, and configuration details recorded at the start of troubleshooting.
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