Added environment.yml for Binder; Tweaked tutorials and README

README.md

@@ -12,9 +12,7 @@ Ensemble Molecular Dynamics
 [![Downloads](https://static.pepy.tech/badge/ensemble-md)](https://pepy.tech/project/ensemble-md)
 [![Twitter Follow](https://img.shields.io/twitter/follow/WeiTseHsu?style=social)](https://twitter.com/WeiTseHsu)
 
-`ensemble_md` is a Python package that provides methods for setting up, running, and analyzing GROMACS simulation ensembles. Currently, the package implements all the necessary algorithms for running synchronous replica exchange (REX) of expanded ensembles (EE), abbreviated as REXEE, as well as its multi-topology (MT) variation MT-REXEE. Our future work includes implementing asynchronous REXEE and other possible variations of the REXEE method.
-
-For installation instructions, theory overview, tutorials, and API references, please visit the [documentation](https://ensemble-md.readthedocs.io/en/latest/?badge=latest).
+`ensemble_md` is a Python package that provides methods for setting up, running, and analyzing GROMACS simulation ensembles. Currently, the package implements all the necessary algorithms for running synchronous replica exchange (REX) of expanded ensembles (EE), abbreviated as REXEE, as well as its multi-topology (MT) variation MT-REXEE. Our future work includes implementing asynchronous REXEE and other possible variations of the REXEE method. For installation instructions, theory overview, tutorials, and API references, please visit the [documentation](https://ensemble-md.readthedocs.io/en/latest/?badge=latest).
 
 ### Copyright
 

docs/examples/run_REXEE.ipynb

@@ -19,15 +19,58 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "id": "83273ada",
-   "metadata": {
-    "vscode": {
-     "languageId": "plaintext"
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "             :-) GROMACS - gmx, 2022.3-dev-20230426-4eabaf582b (-:\n",
+      "\n",
+      "Executable:   /usr/local/bin/gmx\n",
+      "Data prefix:  /usr/local\n",
+      "Working dir:  /Users/Wei-TseHsu/Documents/Life_in_CU_Bouler/Research_in_Shirts_Lab/ensemble_md/docs/examples\n",
+      "Command line:\n",
+      "  gmx\n",
+      "\n",
+      "SYNOPSIS\n",
+      "\n",
+      "gmx [-[no]h] [-[no]quiet] [-[no]version] [-[no]copyright] [-nice <int>]\n",
+      "    [-[no]backup]\n",
+      "\n",
+      "OPTIONS\n",
+      "\n",
+      "Other options:\n",
+      "\n",
+      " -[no]h                     (no)\n",
+      "           Print help and quit\n",
+      " -[no]quiet                 (no)\n",
+      "           Do not print common startup info or quotes\n",
+      " -[no]version               (no)\n",
+      "           Print extended version information and quit\n",
+      " -[no]copyright             (no)\n",
+      "           Print copyright information on startup\n",
+      " -nice   <int>              (19)\n",
+      "           Set the nicelevel (default depends on command)\n",
+      " -[no]backup                (yes)\n",
+      "           Write backups if output files exist\n",
+      "\n",
+      "Additional help is available on the following topics:\n",
+      "    commands    List of available commands\n",
+      "    selections  Selection syntax and usage\n",
+      "To access the help, use 'gmx help <topic>'.\n",
+      "For help on a command, use 'gmx help <command>'.\n",
+      "\n",
+      "GROMACS reminds you: \"I've Got Two Turntables and a Microphone\" (B. Hansen)\n",
+      "\n"
+     ]
     }
-   },
-   "outputs": [],
-   "source": []
+   ],
+   "source": [
+    "!gmx"
+   ]
   },
   {
    "cell_type": "markdown",
@@ -78,7 +121,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.12"
+   "version": "3.9.15"
   }
  },
  "nbformat": 4,

environment.yml

@@ -0,0 +1,8 @@
+name: tutorials
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - gromacs=2023.3=nompi*
+  - ensemble-md
+  - nglview