test_peters_long_range_speedup.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "970ed216",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.\n"
     ]
    }
   ],
   "source": [
    "import time\n",
    "import os\n",
    "import pickle\n",
    "\n",
    "from simtk.openmm import XmlSerializer\n",
    "from simtk import openmm\n",
    "from simtk.openmm import app, unit\n",
    "import openmmtools"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "269645ac",
   "metadata": {},
   "source": [
    "# Check computation time for setUseDispersionCorrection(True) for only the NonbondedForce that contains nonalchemical atoms, but not the CustomNonbondedForce that contains alchemical atoms"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "378e7055",
   "metadata": {},
   "source": [
    "Use long-range env"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "09632b1e",
   "metadata": {},
   "outputs": [],
   "source": [
    "with open('rbd_ace2_example/rbd_ace2_hybrid_system.xml', 'r') as f:\n",
    "    system = XmlSerializer.deserialize(f.read())\n",
    "with open('rbd_ace2_example/rbd_ace2_state.xml', 'r') as f:\n",
    "    state = XmlSerializer.deserialize(f.read())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "0848171e",
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[<openmm.openmm.MonteCarloBarostat; proxy of <Swig Object of type 'OpenMM::MonteCarloBarostat *' at 0x2b04dbf2eed0> >,\n",
       " <openmm.openmm.CustomBondForce; proxy of <Swig Object of type 'OpenMM::CustomBondForce *' at 0x2b04dbf2e1b0> >,\n",
       " <openmm.openmm.HarmonicBondForce; proxy of <Swig Object of type 'OpenMM::HarmonicBondForce *' at 0x2b04dbf2e0f0> >,\n",
       " <openmm.openmm.CustomAngleForce; proxy of <Swig Object of type 'OpenMM::CustomAngleForce *' at 0x2b051d42dba0> >,\n",
       " <openmm.openmm.HarmonicAngleForce; proxy of <Swig Object of type 'OpenMM::HarmonicAngleForce *' at 0x2b051d42de10> >,\n",
       " <openmm.openmm.CustomTorsionForce; proxy of <Swig Object of type 'OpenMM::CustomTorsionForce *' at 0x2b051d42d8d0> >,\n",
       " <openmm.openmm.PeriodicTorsionForce; proxy of <Swig Object of type 'OpenMM::PeriodicTorsionForce *' at 0x2b051d42dcf0> >,\n",
       " <openmm.openmm.NonbondedForce; proxy of <Swig Object of type 'OpenMM::NonbondedForce *' at 0x2b051d42d120> >,\n",
       " <openmm.openmm.CustomNonbondedForce; proxy of <Swig Object of type 'OpenMM::CustomNonbondedForce *' at 0x2b051d42da80> >,\n",
       " <openmm.openmm.CustomBondForce; proxy of <Swig Object of type 'OpenMM::CustomBondForce *' at 0x2b051d42dc90> >]"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "system.getForces()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "aacc7cd7",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "True"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "system.getForce(7).getUseDispersionCorrection()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "a2eda49f",
   "metadata": {},
   "outputs": [],
   "source": [
    "system.getForce(8).setUseLongRangeCorrection(False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "b48b609f",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Set up integrator\n",
    "integrator = openmmtools.integrators.LangevinIntegrator(temperature=300 * unit.kelvin, \n",
    "                                                        collision_rate=1 / unit.picoseconds, \n",
    "                                                        timestep=4 * unit.femtoseconds)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "8e72cca6",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Set up context\n",
    "platform_name = 'CUDA'\n",
    "platform = openmm.Platform.getPlatformByName(platform_name)\n",
    "if platform_name in ['CUDA', 'OpenCL']:\n",
    "    platform.setPropertyDefaultValue('Precision', 'mixed')\n",
    "if platform_name in ['CUDA']:\n",
    "    platform.setPropertyDefaultValue('DeterministicForces', 'true')\n",
    "context = openmm.Context(system, integrator, platform)\n",
    "context.setPeriodicBoxVectors(*state.getPeriodicBoxVectors())\n",
    "context.setPositions(state.getPositions())\n",
    "context.setVelocitiesToTemperature(300 * unit.kelvin)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "8381169b",
   "metadata": {},
   "outputs": [],
   "source": [
    "nsteps = 100\n",
    "initial_time = time.time()\n",
    "for step in range(nsteps):\n",
    "    context.setParameter('lambda_sterics_insert', (step + 1) * 0.01)\n",
    "    integrator.step(1)\n",
    "elapsed_time = (time.time() - initial_time) * unit.seconds"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "6ec993d7",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Quantity(value=8.10090708732605, unit=second)"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "elapsed_time"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "8bbdd964",
   "metadata": {},
   "source": [
    "# Check computation time for setLongRangeCorrection(True) for both CustomNonbondedForces"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "277b2307",
   "metadata": {},
   "source": [
    "Use long-range env"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "9e939bce",
   "metadata": {},
   "outputs": [],
   "source": [
    "with open('rbd_ace2_example/rbd_ace2_hybrid_system.xml', 'r') as f:\n",
    "    system = XmlSerializer.deserialize(f.read())\n",
    "with open('rbd_ace2_example/rbd_ace2_state.xml', 'r') as f:\n",
    "    state = XmlSerializer.deserialize(f.read())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "4f66d4b3",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "True"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "system.getForce(7).getUseDispersionCorrection()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "0c8fc258",
   "metadata": {},
   "outputs": [],
   "source": [
    "system.getForce(8).setUseLongRangeCorrection(True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "2bae6f98",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Set up integrator\n",
    "integrator = openmmtools.integrators.LangevinIntegrator(temperature=300 * unit.kelvin, \n",
    "                                                        collision_rate=1 / unit.picoseconds, \n",
    "                                                        timestep=4 * unit.femtoseconds)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "881624d3",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Set up context\n",
    "platform_name = 'CUDA'\n",
    "platform = openmm.Platform.getPlatformByName(platform_name)\n",
    "if platform_name in ['CUDA', 'OpenCL']:\n",
    "    platform.setPropertyDefaultValue('Precision', 'mixed')\n",
    "if platform_name in ['CUDA']:\n",
    "    platform.setPropertyDefaultValue('DeterministicForces', 'true')\n",
    "context = openmm.Context(system, integrator, platform)\n",
    "context.setPeriodicBoxVectors(*state.getPeriodicBoxVectors())\n",
    "context.setPositions(state.getPositions())\n",
    "context.setVelocitiesToTemperature(300 * unit.kelvin)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "aadbe82a",
   "metadata": {},
   "outputs": [],
   "source": [
    "nsteps = 100\n",
    "initial_time = time.time()\n",
    "for step in range(nsteps):\n",
    "    context.setParameter('lambda_sterics_insert', (step + 1) * 0.01)\n",
    "    integrator.step(1)\n",
    "elapsed_time = (time.time() - initial_time) * unit.seconds"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "id": "57ee6d31",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Quantity(value=36.05855202674866, unit=second)"
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "elapsed_time"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "8c22e1d5",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "id": "e26b353e",
   "metadata": {},
   "source": [
    "# Check computation time for setLongRangeCorrection(True) for both CustomNonbondedForces (and with Peter's fix)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "99e6326c",
   "metadata": {},
   "source": [
    "Use long-range-peter env"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "f3c7ac6d",
   "metadata": {},
   "outputs": [],
   "source": [
    "with open('rbd_ace2_example/rbd_ace2_hybrid_system.xml', 'r') as f:\n",
    "    system = XmlSerializer.deserialize(f.read())\n",
    "with open('rbd_ace2_example/rbd_ace2_state.xml', 'r') as f:\n",
    "    state = XmlSerializer.deserialize(f.read())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "64722b8a",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "True"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "system.getForce(7).getUseDispersionCorrection()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "408abbbe",
   "metadata": {},
   "outputs": [],
   "source": [
    "system.getForce(8).setUseLongRangeCorrection(True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "13c8b1ce",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Set up integrator\n",
    "integrator = openmmtools.integrators.LangevinIntegrator(temperature=300 * unit.kelvin, \n",
    "                                                        collision_rate=1 / unit.picoseconds, \n",
    "                                                        timestep=4 * unit.femtoseconds)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "7d428b9f",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Set up context\n",
    "platform_name = 'CUDA'\n",
    "platform = openmm.Platform.getPlatformByName(platform_name)\n",
    "if platform_name in ['CUDA', 'OpenCL']:\n",
    "    platform.setPropertyDefaultValue('Precision', 'mixed')\n",
    "if platform_name in ['CUDA']:\n",
    "    platform.setPropertyDefaultValue('DeterministicForces', 'true')\n",
    "context = openmm.Context(system, integrator, platform)\n",
    "context.setPeriodicBoxVectors(*state.getPeriodicBoxVectors())\n",
    "context.setPositions(state.getPositions())\n",
    "context.setVelocitiesToTemperature(300 * unit.kelvin)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "f542945d",
   "metadata": {},
   "outputs": [],
   "source": [
    "nsteps = 100\n",
    "initial_time = time.time()\n",
    "for step in range(nsteps):\n",
    "    context.setParameter('lambda_sterics_insert', (step + 1) * 0.01)\n",
    "    integrator.step(1)\n",
    "elapsed_time = (time.time() - initial_time) * unit.seconds"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "23a2999c",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Quantity(value=12.859097957611084, unit=second)"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "elapsed_time"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "973923ff",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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