openff-molecule-output-lots-of-ways.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Using OpenForce toolkit to parameterize molecules"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 69,
   "metadata": {},
   "outputs": [],
   "source": [
    "from openff.toolkit import Molecule, Topology, ForceField\n",
    "from openff.interchange import Interchange\n",
    "from openff.units import unit, Quantity\n",
    "from openff.toolkit.utils.toolkits import NAGLToolkitWrapper\n",
    "import numpy as np"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Define a molecule via SMILES 1D representation"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 70,
   "metadata": {},
   "outputs": [
    {
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     "execution_count": 70,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mol_smiles = \"C1CCCCC1\" # cyclohexane\n",
    "\n",
    "monomer = Molecule.from_smiles(mol_smiles) \n",
    "monomer.visualize()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 71,
   "metadata": {},
   "outputs": [],
   "source": [
    "# assign a force field\n",
    "sage = ForceField(\"openff-2.2.0.offxml\")\n",
    "# big box\n",
    "cubic_box = unit.Quantity(50 * np.eye(3), unit.angstrom)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 72,
   "metadata": {},
   "outputs": [],
   "source": [
    "# use RDkit to generate a conformer\n",
    "monomer.generate_conformers(n_conformers=1)\n",
    "\n",
    "# create the internal representation\n",
    "topology = Topology.from_molecules(monomer)\n",
    "\n",
    "# create the interchange object. Note- is parameterizing with AM1-BCC\n",
    "solute_interchange = Interchange.from_smirnoff(topology=[monomer], \n",
    "                                                   force_field=sage, box = cubic_box)\n",
    "\n",
    "# approximately minimize energy with OpenMM\n",
    "solute_interchange.minimize()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 94,
   "metadata": {},
   "outputs": [],
   "source": [
    "# lammps files\n",
    "solute_interchange.to_lammps('monomer.lmp')\n",
    "\n",
    "# gromacs files\n",
    "solute_interchange.to_gro('monomer.gro')\n",
    "solute_interchange.to_top('monomer.top')\n",
    "\n",
    "# amber files\n",
    "solute_interchange.to_prmtop('monomer.prmtop') \n",
    "solute_interchange.to_inpcrd(\"monomer.inpcrd\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Version that packs a box with the designated molecule."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 74,
   "metadata": {},
   "outputs": [],
   "source": [
    "from openff.interchange.components._packmol import pack_box"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 75,
   "metadata": {},
   "outputs": [],
   "source": [
    "n_solute = 200\n",
    "#Define the box\n",
    "# this box may be too big, will need to be equilibrated\n",
    "cubic_box = unit.Quantity(35 * np.eye(3), unit.angstrom)\n",
    "\n",
    "monomer.generate_conformers(n_conformers=1) \n",
    "# above generates a single conformation, could potentially make a more complicated version\n",
    "# with multiple configurations?\n",
    "\n",
    "packed_topology = pack_box(\n",
    "        molecules=[monomer],\n",
    "        number_of_copies=[n_solute],\n",
    "        solute=None,\n",
    "        tolerance=1.0*unit.angstrom,\n",
    "        box_vectors=cubic_box,\n",
    "    )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 76,
   "metadata": {},
   "outputs": [],
   "source": [
    "packed_interchange = Interchange.from_smirnoff(\n",
    "            force_field=ForceField(\"openff-2.2.0.offxml\"),\n",
    "            topology=packed_topology, box=cubic_box)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 77,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Minimize with OpenMM\n",
    "packed_interchange.minimize()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 78,
   "metadata": {},
   "outputs": [],
   "source": [
    "# create lammps files\n",
    "packed_interchange.to_lammps('monomer_packed.lmp')\n",
    "\n",
    "# create gromacs files\n",
    "packed_interchange.to_gro('monomer_packed.gro')\n",
    "packed_interchange.to_top('monomer_packed.top')\n",
    "\n",
    "# create amber files\n",
    "packed_interchange.to_prmtop('monomer_packed.prmtop') \n",
    "packed_interchange.to_inpcrd(\"monomer_packed.inpcrd\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Solvating the molecule in water"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 79,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Construct a water molecule\n",
    "water = Molecule.from_smiles(\"O\")\n",
    "water.generate_conformers(n_conformers=1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 80,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Pack the box with an arbitrary number of water around the solute.\n",
    "\n",
    "cubic_box = unit.Quantity(30 * np.eye(3), unit.angstrom)\n",
    "n_water = 900\n",
    "\n",
    "from openff.interchange.components._packmol import pack_box\n",
    "packed_topology = pack_box(\n",
    "    molecules=[water],\n",
    "    number_of_copies=[n_water],\n",
    "    solute=Topology.from_molecules(monomer),\n",
    "    tolerance=0.5*unit.angstrom,\n",
    "    box_vectors=cubic_box,\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 81,
   "metadata": {},
   "outputs": [],
   "source": [
    "solvated_interchange = Interchange.from_smirnoff(\n",
    "    force_field=ForceField(\"openff-2.2.0.offxml\",\"opc3.offxml\"),\n",
    "    topology=packed_topology,\n",
    "    box=cubic_box\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 82,
   "metadata": {},
   "outputs": [],
   "source": [
    "# approximately minimize energy with OpenMM\n",
    "solute_interchange.minimize()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 83,
   "metadata": {},
   "outputs": [],
   "source": [
    "# lammps files\n",
    "solvated_interchange.to_lammps('solvated_molecule.lmp')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 84,
   "metadata": {},
   "outputs": [],
   "source": [
    "# gromacs files\n",
    "solvated_interchange.to_gro('solvated_molecule.gro')\n",
    "solvated_interchange.to_top('solvated_molecule.top')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 85,
   "metadata": {},
   "outputs": [],
   "source": [
    "# for kicks, amber files\n",
    "solvated_interchange.to_prmtop('solvated_molecule.prmtop') \n",
    "solvated_interchange.to_inpcrd(\"solvated_molecule.inpcrd\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Creating a mixture"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 86,
   "metadata": {},
   "outputs": [
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       "<path class=\"atom-18\" d=\"M 35.7 152.1 L 39.6 152.1 L 39.6 164.2 L 54.1 164.2 L 54.1 152.1 L 57.9 152.1 L 57.9 180.5 L 54.1 180.5 L 54.1 167.4 L 39.6 167.4 L 39.6 180.5 L 35.7 180.5 L 35.7 152.1 \" fill=\"#000000\"/>\n",
       "<path class=\"atom-19\" d=\"M 110.5 79.3 L 114.4 79.3 L 114.4 91.3 L 128.8 91.3 L 128.8 79.3 L 132.7 79.3 L 132.7 107.6 L 128.8 107.6 L 128.8 94.5 L 114.4 94.5 L 114.4 107.6 L 110.5 107.6 L 110.5 79.3 \" fill=\"#000000\"/>\n",
       "</svg>"
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      "text/plain": [
       "<IPython.core.display.SVG object>"
      ]
     },
     "execution_count": 86,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "monomer2 = Molecule.from_smiles(\"CCCCCC\")\n",
    "monomer2.generate_conformers(n_conformers=1)\n",
    "monomer2.visualize()\n",
    "# use RDkit to generate a conformer\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 87,
   "metadata": {},
   "outputs": [
    {
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      ]
     },
     "execution_count": 87,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "monomer3 = Molecule.from_smiles(\"C=CC(CS)C=C\")\n",
    "monomer3.generate_conformers(n_conformers=1)\n",
    "monomer3.visualize()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 88,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Pack the box with all three solutes\n",
    "\n",
    "# box is probably too big\n",
    "cubic_box = unit.Quantity(40 * np.eye(3), unit.angstrom)\n",
    "n_monomer = 100\n",
    "n_monomer2 = 100\n",
    "n_monomer3 = 100\n",
    "\n",
    "from openff.interchange.components._packmol import pack_box\n",
    "packed_mixture_topology = pack_box(\n",
    "    molecules=[monomer,monomer2,monomer3],\n",
    "    number_of_copies=[n_monomer,n_monomer2,n_monomer3],\n",
    "    solute=None,\n",
    "    tolerance=1.0*unit.angstrom,\n",
    "    box_vectors=cubic_box,\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 89,
   "metadata": {},
   "outputs": [],
   "source": [
    "mixture_interchange = Interchange.from_smirnoff(\n",
    "    force_field=ForceField(\"openff-2.2.0.offxml\",\"opc3.offxml\"),\n",
    "    topology=packed_mixture_topology,\n",
    "    box=cubic_box\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 90,
   "metadata": {},
   "outputs": [],
   "source": [
    "# approximately minimize energy with OpenMM\n",
    "mixture_interchange.minimize()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 91,
   "metadata": {},
   "outputs": [],
   "source": [
    "# lammps files\n",
    "mixture_interchange.to_lammps('mixture.lmp')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 92,
   "metadata": {},
   "outputs": [],
   "source": [
    "# gromacs files\n",
    "mixture_interchange.to_gro('mixture.gro')\n",
    "solvated_interchange.to_top('mixture.top')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 93,
   "metadata": {},
   "outputs": [],
   "source": [
    "# for kicks, amber files\n",
    "mixture_interchange.to_prmtop('mixture.prmtop') \n",
    "mixture_interchange.to_inpcrd(\"mixture.inpcrd\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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