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Merge pull request #18 from dwhswenson/openmm-setup
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Switch builder.openmm.org => OpenMM-Setup
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dwhswenson authored Nov 11, 2021
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"source": [
"The next cell shows you how to set up several things specific to OpenMM. We'll be running in the $NVT$ ensemble, with $T=300 K$. We're using the [Velocity Verlet with Velocity Randomization (VVVR) integrator](http://arxiv.org/abs/1301.3800), which simulates Langevin dynamics. Note that the integrator itself comes from [`openmmtools`](https://github.com/choderalab/openmmtools), a library that extends OpenMM. You should always use a reversible integrator when performing path sampling simulations. The default integrators in OpenMM are leapfrog-based, and therefore not reversible.\n",
"\n",
"You can learn a lot more about setting up OpenMM simulations from the [OpenMM documentation](http://docs.openmm.org/). However, it is often even easier to use the [OpenMM Script Builder](http://builder.openmm.org/) to learn how to set up the simulation the way you'd like."
"You can learn a lot more about setting up OpenMM simulations from the [OpenMM documentation](http://docs.openmm.org/). However, it is often even easier to use [OpenMM-Setup](https://github.com/openmm/openmm-setup/) to learn how to set up the simulation the way you'd like."
]
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{
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