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Documentation updates in README.
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jchodera committed Jun 21, 2015
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# Various Python tools for OpenMM

## `openmmtools.testsystems`
## Integrators

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

These classes will also contain the member functions that calculate known
analytical properties of these systems, enabling the proper testing.
## Test system suite

## `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

A script that may be useful in testing your OpenMM installation is installed:
## OpenMM testing scripts

`scripts/` contains a script that may be useful in testing your OpenMM installation is installed:

* `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.

This is installed onto the command line when the repository is installed.

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