tweaks

README.md

@@ -195,7 +195,7 @@ New MDP file options (subject to change as we work with GROMACS developers):
 ```
 IMD-group               = <group> ; Use 'System' to send the entire system via IMD (inherited from IMDv2)
 IMD-version             = <2 | 3> ; Defaults to 2 for backwards compatibility
-IMD-nst                 = <nst>   ; Number of integration steps between simulation frames communicated via IMD, defaults to 
+IMD-nst                 = <nst>   ; Number of integration steps between simulation frames communicated via IMD, defaults to 100
 IMD-time                = <yes | no> ; Whether to send time and step information via IMD, defaults to 'no'
 IMD-box                 = <yes | no> ; Whether to send box dimension information via IMD, defaults to 'no'
 IMD-coords              = <yes | no> ; Whether to send atomic coordinate information via IMD, defaults to 'no'

streaming-101/imd-mda/imd-mda.ipynb

@@ -171,13 +171,21 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 12,
    "metadata": {
     "slideshow": {
      "slide_type": "fragment"
     }
    },
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "The position of the first atom is: [43.99073  29.392868 30.756462]\r"
+     ]
+    }
+   ],
    "source": [
     "import imdclient\n",
     "\n",
@@ -186,6 +194,7 @@
     "    while True:\n",
     "        try:\n",
     "            frame = client.get_imdframe()\n",
+    "            print(f\"The position of the first atom is: {frame.positions[0]}\", end=\"\\r\")\n",
     "        except EOFError:\n",
     "            break"
    ]