From 663288301fd741d2706858753709da35234605ac Mon Sep 17 00:00:00 2001 From: sroet Date: Thu, 13 Jan 2022 15:11:30 +0100 Subject: [PATCH 1/2] update simtk to openmm --- 1_tps_sampling_tutorial.ipynb | 6 +++--- 5_custom_shooting_setup.ipynb | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/1_tps_sampling_tutorial.ipynb b/1_tps_sampling_tutorial.ipynb index 195bfe1..42cc9c9 100644 --- a/1_tps_sampling_tutorial.ipynb +++ b/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", diff --git a/5_custom_shooting_setup.ipynb b/5_custom_shooting_setup.ipynb index 13f90dc..28eeb99 100644 --- a/5_custom_shooting_setup.ipynb +++ b/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" ] }, From 312f4f12010b8f9afee1511615aa1a031b0cef9c Mon Sep 17 00:00:00 2001 From: sroet Date: Thu, 13 Jan 2022 15:14:10 +0100 Subject: [PATCH 2/2] update molsim in readme --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index e20ddb9..5925f5f 100644 --- a/README.md +++ b/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