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TIP3P water example #1

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311 changes: 311 additions & 0 deletions tip3p-water-box/topology-water-box-gromacs.ipynb
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{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Water Box Example -- GROMACS\n",
"\n",
"In this simulation a GROMACS simulation of tip3p water is set up and run using `mBuild` and `GMSO`."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"import mbuild as mb\n",
"\n",
"import gmso\n",
"from gmso import ForceField\n",
"from gmso.external import convert_mbuild\n",
"from gmso.formats.gro import write_gro\n",
"from gmso.formats.top import write_top"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"%%writefile spce.mol2\n",
"@<TRIPOS>MOLECULE\n",
"RES\n",
"3 0 1 0 1\n",
"SMALL\n",
"NO_CHARGES\n",
"@<TRIPOS>CRYSIN\n",
" 3.0130 3.0130 3.0130 90.0000 90.0000 90.0000 1 1\n",
"@<TRIPOS>ATOM\n",
" 1 O 0.0000 0.0000 0.0000 O 1 RES \n",
" 2 H -0.6126 -0.7357 0.0000 H 1 RES \n",
" 3 H -0.5469 0.7762 0.0000 H 1 RES \n",
"@<TRIPOS>BOND\n",
" 1 1 2 1\n",
" 2 1 3 1\n",
"@<TRIPOS>SUBSTRUCTURE\n",
" 1 RES 1 RESIDUE 0 **** ROOT 0"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# Load in single water (SPC/E) structure\n",
"\n",
"water = mb.load(\"spce.mol2\")\n",
"water = water.children[0]\n",
"water.name = \"water\"\n",
"\n",
"# element_map = which site name corresponds to which atom_type name. \n",
"# In the future atomtyping will be done through foyer. \n",
"element_map = {\"O\": \"opls_116\",\n",
" \"H\": \"opls_117\"}"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# Fill a box with 1000 water molecule\n",
"\n",
"water_box = mb.fill_box(\n",
" compound=water, \n",
" n_compounds=1000,\n",
" density=1000,\n",
")"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# Write out the SPC/E water xml file\n",
"%%writefile spce.xml\n",
"<?xml version='1.0' encoding='UTF-8'?>\n",
"<ForceField name=\"spce\" version=\"0.0.1\">\n",
" <FFMetaData>\n",
" <Units energy=\"kcal/mol\" mass=\"amu\" charge=\"elementary_charge\" distance=\"nm\"/>\n",
" </FFMetaData>\n",
" <AtomTypes expression=\"4 * epsilon * ((sigma/r)**12 - (sigma/r)**6)\">\n",
" <ParametersUnitDef parameter=\"epsilon\" unit=\"kJ/mol\"/>\n",
" <ParametersUnitDef parameter=\"sigma\" unit=\"nm\"/>\n",
" <AtomType name=\"opls_116\" atomclass=\"OW\" element=\"O\" charge=\"-0.8476\" mass=\"15.999\" definition=\"O\">\n",
" <Parameters>\n",
" <Parameter name=\"epsilon\" value=\"0.650194\"/>\n",
" <Parameter name=\"sigma\" value=\"0.316557\"/>\n",
" </Parameters>\n",
" </AtomType>\n",
" <AtomType name=\"opls_117\" atomclass=\"HW\" element=\"H\" charge=\"0.4238\" mass=\"1.00784\" definition=\"H\">\n",
" <Parameters>\n",
" <Parameter name=\"epsilon\" value=\"0.0\"/>\n",
" <Parameter name=\"sigma\" value=\"0.1\"/>\n",
" </Parameters>\n",
" </AtomType>\n",
" </AtomTypes>\n",
" <BondTypes expression=\"0.5 * k * (r-r_eq)**2\">\n",
" <ParametersUnitDef parameter=\"k\" unit=\"kJ/mol/nm**2\"/>\n",
" <ParametersUnitDef parameter=\"r_eq\" unit=\"nm\"/>\n",
" <BondType name=\"BondType-Harmonic-1\" type1=\"opls_116\" type2=\"opls_117\">\n",
" <Parameters>\n",
" <Parameter name=\"k\" value=\"345000.0\"/>\n",
" <Parameter name=\"r_eq\" value=\"0.1\"/>\n",
" </Parameters>\n",
" </BondType>\n",
" </BondTypes>\n",
" <AngleTypes expression=\"0.5 * k * (theta - theta_eq)**2\">\n",
" <ParametersUnitDef parameter=\"k\" unit=\"kJ/mol/degree**2\"/>\n",
" <ParametersUnitDef parameter=\"theta_eq\" unit=\"degree\"/>\n",
" <AngleType name=\"AngleType-Harmonic-1\" type1=\"opls_116\" type2=\"opls_117\" type3=\"opls_117\">\n",
" <Parameters>\n",
" <Parameter name=\"k\" value=\"383.0\"/>\n",
" <Parameter name=\"theta_eq\" value=\"1.91061193\"/>\n",
" </Parameters>\n",
" </AngleType>\n",
" </AngleTypes>\n",
"</ForceField>"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# Load in topology forcefield\n",
"\n",
"forcefield = ForceField(\"spce.xml\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# Generate a topology from the mbuild compound\n",
"\n",
"top = convert_mbuild.from_mbuild(water_box)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# Assign atom types\n",
"for atom in top.sites:\n",
" atom.atom_type = forcefield.atom_types[element_map[atom.name]]\n",
" \n",
"# Assign bond types\n",
"for bond in top.bonds:\n",
" bond.bond_type = bond.connection_type = forcefield.bond_types[\"opls_116~opls_117\"]\n",
"\n",
"# Create angles with correct atom type and add to top\n",
"for subtop in top.subtops:\n",
" angle = gmso.core.angle.Angle(\n",
" connection_members=[site for site in subtop.sites],\n",
" name=\"opls_116~opls_117~opls_117\",\n",
" connection_type=forcefield.angle_types[\"opls_116~opls_117~opls_117\"]\n",
" )\n",
" top.add_connection(angle, update_types=False)\n",
"\n",
"top.update_topology()"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# Write out gro and top files\n",
"\n",
"write_gro(top, \"system.gro\")\n",
"write_top(top, \"system.top\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# Lets look at the TOP file\n",
"\n",
"!cat system.top"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# Write out an MDP file for an NPT simulation\n",
"%%writefile npt.mdp\n",
"constraints = h-bonds\n",
"integrator = md\n",
"nsteps = 1000000\n",
"dt = 0.001\n",
"\n",
"nstxtcout = 10\n",
"nstenergy = 1000\n",
"nstlog = 1000\n",
"\n",
"cutoff-scheme = Verlet\n",
"ns_type = grid\n",
"nstlist = 10\n",
"rcoulomb = 0.8\n",
"rvdw = 0.8 \n",
"\n",
"coulombtype = PME\n",
"\n",
"gen_vel = yes\n",
"\n",
"tcoupl = nose-hoover\n",
"tc-grps = System\n",
"tau_t = 1\n",
"ref_t = 300\n",
"\n",
"pcoupl = Parrinello-Rahman\n",
"pcoupltype = isotropic\n",
"tau-p = 10\n",
"ref-p = 1\n",
"compressibility = 1e-5"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"!gmx grompp -f npt.mdp -c system.gro -p system.top -o npt.tpr -maxwarn 2"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"!gmx mdrun -v -s npt.tpr"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"import mdtraj as md\n",
"traj = md.load(\"traj_comp.xtc\", top=\"system.gro\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"traj"
]
},
{
"cell_type": "raw",
"metadata": {},
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.2"
}
},
"nbformat": 4,
"nbformat_minor": 2
}