Merge pull request #19 from sroet/openmm_76

Author: dwhswenson

1_tps_sampling_tutorial.ipynb

@@ -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",

5_custom_shooting_setup.ipynb

@@ -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"
    ]
   },

README.md

@@ -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