Created using Colab

pablo-arantes · Jan 22, 2025 · 27ebc24 · 27ebc24
1 parent e231cbd
commit 27ebc24
Showing 1 changed file with 3 additions and 2 deletions.
diff --git a/Gromacs_inputs.ipynb b/Gromacs_inputs.ipynb
@@ -128,7 +128,7 @@
         "import pytraj as pt\n",
         "subprocess.run(\"pip -q install py3Dmol\", shell=True)\n",
         "subprocess.run(\"pip install git+https://github.com/pablo-arantes/biopandas\", shell=True)\n",
-        "subprocess.run(\"mamba install openmm=7.7.0\", shell=True)\n",
+        "subprocess.run(\"mamba install openmm\", shell=True)\n",
         "subprocess.run(\"pip install --upgrade MDAnalysis==2.4.2\", shell=True)\n",
         "\n",
         "#load dependencies\n",
@@ -571,7 +571,8 @@
         "#     simulation.context.setPeriodicBoxVectors(topologyfile, periodicBoxVectors=gro.getPeriodicBoxVectors())\n",
         "\n",
         "print(\"\\t- Energy minimization: \" + str(Minimization_steps) + \" steps\")\n",
-        "simulation.minimizeEnergy(tolerance=10*kilojoule/mole, maxIterations=int(Minimization_steps))\n",
+        "simulation.minimizeEnergy(tolerance=10*kilojoule/mole/nanometer, maxIterations=int(Minimization_steps))\n",
+        "\n",
         "print(\"\\t-> Potential Energy = \" + str(simulation.context.getState(getEnergy=True).getPotentialEnergy()))\n",
         "\n",
         "print(\"\\t- Setting initial velocities...\")\n",