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# Various Python tools for OpenMM | ||
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## `openmmtools.testsystems` | ||
## Integrators | ||
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This repository contains a suite of molecular systems that can be used | ||
for the testing of various molecular mechanics related software. The | ||
idea is that this repository will host a number classes that generate | ||
OpenMM objects for simulating the desired systems. | ||
This repository contains a number of additional integrators for OpenMM in `openmmtools.integrators`, including | ||
* `MTSIntegrator` - a multiple timestep integrator | ||
* `DummyIntegrator` - a "dummy" integrator that does not update positions | ||
* `GradientDescentMinimizationIntegrator` - a simple gradient descent minimizer (without line search) | ||
* `VelocityVerletIntegrator` - a velocity Verlet integrator | ||
* `AndersenVelocityVerletIntegrator` - a velocity Verlet integrator with Andersen thermostat using per-particle collisions | ||
* `MetropolisMonteCarloIntegrator` - a Metropolis Monte Carlo integrator that uses Gaussian displacement trials | ||
* `HMCIntegrator` - a hybrid Monte Carlo (HMC) integrator | ||
* `GHMCIntegrator` - a generalized hybrid Monte Carlo (GHMC) integrator | ||
* `VVVRIntegrator` - a velocity Verlet with velocity randomization (VVVR) integrator | ||
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These classes will also contain the member functions that calculate known | ||
analytical properties of these systems, enabling the proper testing. | ||
## Test system suite | ||
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## `scripts` | ||
The `openmmtools.testsystems` module contains a large suite of test systems---including many with simple exactly-computable properties---that can be used to test molecular simulation algorith,s | ||
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A script that may be useful in testing your OpenMM installation is installed: | ||
## OpenMM testing scripts | ||
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`scripts/` contains a script that may be useful in testing your OpenMM installation is installed: | ||
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* `test-openmm-platforms` will test the various platforms available to OpenMM to ensure that all systems in `openmmtools.testsystems` give consistent potential energies. | ||
If differences in energies in excess of `ENERGY_TOLERANCE` (default: 0.06 kcal/mol) are detected, these systems will be serialized to XML for further debugging. | ||
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This is installed onto the command line when the repository is installed. |