FIX: Fix run settings

openforcefield · Aug 29, 2024 · 7fa5358 · 7fa5358
1 parent c9a4b40
commit 7fa5358
Showing 1 changed file with 9 additions and 9 deletions.
diff --git a/examples/amber/amber.ipynb b/examples/amber/amber.ipynb
@@ -115,8 +115,8 @@
     "&cntrl\n",
     "  imin=0,                ! Run molecular dynamics.\n",
     "  ntx=1,                 ! Take positions from input and generate velocities\n",
-    "  nstlim=1000,           ! Number of MD-steps to be performed.\n",
-    "  dt=0.002,              ! Time step (ps)\n",
+    "  nstlim=500,            ! Number of MD-steps to be performed.\n",
+    "  dt=0.001,              ! Time step (ps), use a low 1 ps timestep to be safe\n",
     "  tempi=300.0,           ! Initial temperature for velocity generation\n",
     "  temp0=300.0,           ! Thermostat temperature\n",
     "  cut=9.0,               ! vdW cutoff (Å)\n",
@@ -126,7 +126,7 @@
     "  ntp=0,                 ! No pressure scaling\n",
     "  iwrap=1,               ! Wrap trajectory coordinates to stay in box\n",
     "  ioutfm=1,              ! Write out netcdf trajectory\n",
-    "  ntwx=1,                ! Frequency to write coordinates\n",
+    "  ntwx=10,               ! Frequency to write coordinates\n",
     "  ntpr=50,               ! Frequency to log energy info\n",
     "  ntc=2,                 ! Constraints on Hydrogen-involving bonds\n",
     "/\n",
@@ -148,11 +148,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "!sander                          \\\n",
-    "    -O                          \\\n",
-    "    -i mysim.in                 \\\n",
-    "    -p mysim.prmtop             \\\n",
-    "    -c mysim_pointenergy.inpcrd \\\n",
+    "!sander                 \\\n",
+    "    -O                  \\\n",
+    "    -i amber.in         \\\n",
+    "    -p mysim.prmtop     \\\n",
+    "    -c mysim.inpcrd     \\\n",
     "    -x trajectory.nc"
    ]
   },
@@ -169,7 +169,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "traj = mdtraj.load(\"trajectory.nc\", top=mdtraj.load_prmtop(\"amber.prmtop\"))\n",
+    "traj = mdtraj.load(\"trajectory.nc\", top=mdtraj.load_prmtop(\"mysim.prmtop\"))\n",
     "nglview.show_mdtraj(traj)"
    ]
   }