adding MEMM project notebook

markovmodel · Feb 21, 2018 · 3466c26 · 3466c26
1 parent 2dcdfde
commit 3466c26
Showing 1 changed file with 196 additions and 0 deletions.
diff --git a/notebooks/MEMM_05_project.ipynb b/notebooks/MEMM_05_project.ipynb
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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# MEMM project: NaCL umbrella sampling"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%matplotlib inline\n",
+    "import matplotlib.pyplot as plt\n",
+    "import matplotlib as mpl\n",
+    "import numpy as np\n",
+    "import pyemma\n",
+    "import mdshare\n",
+    "\n",
+    "mpl.rcParams.update({'font.size': 14})"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Now it is your turn. Below you will find a dataset of a Na-Cl-dimer in TiP3P water; the dataset includes Na-Cl-distance timeseries from NN biased simulations which incrementally pull the ions apart and 20 unbiased simulations started at a Na-Cl-distance of approximately 3.5 Angstrom. The umbrella sampling parameters and the kT value are also given.\n",
+    "\n",
+    "All distances in the dataset are in Angstrom, energies in kcal/mol, and the trajectory timestep is 1 ps."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 18,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "with np.load(mdshare.load('pyemma-tutorial-us-nacl.npz', working_directory='data')) as fh:\n",
+    "    us_trajs = [fh['us_traj_%03d' % i] for i in range(60)]\n",
+    "    us_centers = fh['us_centers'].tolist()\n",
+    "    us_force_constants = fh['us_force_constants'].tolist()\n",
+    "    md_trajs = [fh['md_traj_%03d' % i] for i in range(20)]\n",
+    "    kT = float(fh['kT'])"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Step 1\n",
+    "\n",
+    "You can experiment with visualizations of the raw data or jump straight into the discretization."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# FIXME"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Step 2\n",
+    "Try to apply WHAM to get a quick estimate of the stationary properties of the system. Try only the biased data or use both biased and unbiased."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# FIXME"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Step 3\n",
+    "Now apply DTRAM and estimate the kinetic properties of the system. Remember: kinetics require unbiased data!"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# FIXME"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Step 4\n",
+    "We have unbiased data, so let's build a regular MSM and compare with the MEMM results."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# FIXME"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.6.1"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}