From fda894510910f33640818796d847f9798aad3961 Mon Sep 17 00:00:00 2001 From: "John Chodera (MSKCC)" Date: Sun, 21 Jun 2015 11:09:27 -0400 Subject: [PATCH] Documentation updates in README. --- README.md | 29 +++++++++++++++++++---------- 1 file changed, 19 insertions(+), 10 deletions(-) diff --git a/README.md b/README.md index 663d0582d..8cd26f250 100644 --- a/README.md +++ b/README.md @@ -1,24 +1,33 @@ [![Linux Build Status](https://travis-ci.org/choderalab/openmmtools.png?branch=master)](https://travis-ci.org/choderalab/openmmtools) [![Windows Build status](https://ci.appveyor.com/api/projects/status/80ov9tdffg5jkr7i/branch/master)](https://ci.appveyor.com/project/rmcgibbo/mdtraj-813/branch/master) - [![Binstar Badge](https://binstar.org/omnia/openmmtools/badges/version.svg)](https://binstar.org/omnia/openmmtools) + # 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.