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Jan 13, 2022
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update simtk to openmm #19

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6632883
update simtk to openmm
sroet Jan 13, 2022
312f4f1
update molsim in readme
sroet Jan 13, 2022
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6 changes: 3 additions & 3 deletions 1_tps_sampling_tutorial.ipynb
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Expand Up @@ -33,9 +33,9 @@
"import matplotlib.pyplot as plt\n",
"import numpy as np\n",
"\n",
"from simtk.openmm import app\n",
"import simtk.openmm as mm\n",
"import simtk.unit as unit\n",
"from openmm import app\n",
"import openmm as mm\n",
"import openmm.unit as unit\n",
"import openmmtools\n",
"\n",
"import openpathsampling as paths\n",
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2 changes: 1 addition & 1 deletion 5_custom_shooting_setup.ipynb
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Expand Up @@ -157,7 +157,7 @@
"source": [
"For our two-way shooting, we'll need to create a `TwoWayShootingStrategy`. This will require a modifier; to keep things simple, we'll completely randomize velocities (consistent with a given temperature) using `paths.RandomVelocities`. In order to be consistent between engines, `RandomVelocities` takes its input as the inverse temperature, $\\beta = 1/(k_\\text{B}T)$.\n",
"\n",
"For the toy engine, we can obtain the temperature from `engine.integ.temperature`, and we work in units where $k_\\text{B}=1$, so it is easy to calculate $\\beta$. For other engines, you'll need to use the correct value of $k_\\text{B}$. For OpenMM, you also need to worry about units: use `simtk.unit.BOLTZMANN_CONSTANT_kB`.\n",
"For the toy engine, we can obtain the temperature from `engine.integ.temperature`, and we work in units where $k_\\text{B}=1$, so it is easy to calculate $\\beta$. For other engines, you'll need to use the correct value of $k_\\text{B}$. For OpenMM, you also need to worry about units: use `openmm.unit.BOLTZMANN_CONSTANT_kB`.\n",
"\n"
]
},
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -112,7 +112,7 @@ This tutorial has been used in multiple classes and workshops, including
several E-CAM Extended Software Development Workshops (Leiden, The Netherlands,
2017; Lyon, France, 2019), Master's-level courses in Biomolecular Simulation at
the University of Amsterdam (since 2017), and the CECAM flagship school MolSim
(2021).
(2021-2022).

This tutorial was developed with financial support from the European Union's
Horizon 2020 research and innovation program, under grant agreement No. 676531
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