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https://github.com/openmm/openmm
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393 lines
18 KiB
C++
393 lines
18 KiB
C++
/* -----------------------------------------------------------------------------
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* OpenMM HelloEthane example in C++ (June 2009)
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* -----------------------------------------------------------------------------
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* This is a complete, self-contained "hello world" example demonstrating
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* GPU-accelerated simulation of a system with both bonded and nonbonded forces,
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* using ethane (H3-C-C-H3) in a vacuum as an example. A multi-frame PDB file is
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* written to stdout which can be read by VMD or other visualization tool to
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* produce an animation of the resulting trajectory.
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*
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* Pay particular attention to the handling of units in this example. Incorrect
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* handling of units is a very common error; this example shows how you can
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* continue to work with Amber-style units of Angstroms and kCals while correctly
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* communicating with OpenMM in nanometers and kJoules.
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* -------------------------------------------------------------------------- */
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#include <cstdio>
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#include <string>
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#include <vector>
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// -----------------------------------------------------------------------------
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// MOCK MD CODE
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// -----------------------------------------------------------------------------
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// The code starting here and through main() below is meant to represent in
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// simplified form some pre-existing molecular dynamics code, which defines its
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// own data structures for force fields, the atoms in this simulation, and the
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// simulation parameters, and takes care of recording the trajectory. All this
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// has nothing to do with OpenMM; the OpenMM-dependent code comes later and is
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// clearly marked below.
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// -----------------------------------------------------------------------------
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// MODELING AND SIMULATION PARAMETERS
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const bool UseConstraints = false; // Should we constrain C-H bonds?
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const double StepSizeInFs = 2; // integration step size (fs)
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const double ReportIntervalInFs = 10; // how often to generate PDB frame (fs)
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const double SimulationTimeInPs = 100; // total simulation time (ps)
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static const bool WantEnergy = true;
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// FORCE FIELD DATA
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// For this example we're using a tiny subset of the Amber99 force field.
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// We want to keep the data in the original unit system to avoid conversion
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// bugs; this requires conversion on the way in and out of OpenMM.
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// Amber reduces nonbonded forces between 1-4 bonded atoms.
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const double Coulomb14Scale = 0.5;
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const double LennardJones14Scale = 0.5;
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struct AtomType {
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double mass, charge, vdwRadiusInAngstroms, vdwEnergyInKcal;
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} atomType[] = {/*0 H*/ 1.008, 0.0605, 1.4870, 0.0157,
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/*1 C*/12.011, -.1815, 1.9080, 0.1094};
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const int H = 0, C = 1;
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struct BondType {
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double nominalLengthInAngstroms, stiffnessInKcalPerAngstrom2;
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bool canConstrain;
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} bondType[] = {/*0 CC*/1.526, 310., false,
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/*1 CH*/1.09 , 340., true};
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const int CC = 0, CH = 1;
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struct AngleType {
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double nominalAngleInDegrees, stiffnessInKcalPerRadian2;
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} angleType[] = {/*0 HCC*/109.5, 50.,
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/*1 HCH*/109.5, 35.};
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const int HCC = 0, HCH = 1;
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struct TorsionType {
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int periodicity;
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double phaseInDegrees, amplitudeInKcal;
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} torsionType[] = {/*0 HCCH*/3, 0., 0.150};
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const int HCCH = 0;
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// MOLECULE DATA
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// Now describe an ethane molecule by listing its atoms, bonds, angles, and
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// torsions. We'll provide a default configuration which centers the molecule
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// at (0,0,0) with the C-C bond along the x axis.
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// Use this as an "end of list" marker so that we do not have to count; let the
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// computer do that!
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const int EndOfList=-1;
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struct MyAtomInfo
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{ int type; const char* pdb; double initPosInAng[3]; double posInAng[3];} atoms[] =
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{/*0*/C, " C1 ", { -.7605, 0, 0 }, {0,0,0},
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/*1*/C, " C2 ", { .7605, 0, 0 }, {0,0,0},
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/*2*/H, "1H1 ", {-1.135, 1.03, 0 }, {0,0,0}, // bonded to C1
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/*3*/H, "2H1 ", {-1.135, -.51, .89}, {0,0,0},
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/*4*/H, "3H1 ", {-1.135, -.51,-.89}, {0,0,0},
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/*5*/H, "1H2 ", { 1.135, 1.03, 0 }, {0,0,0}, // bonded to C2
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/*6*/H, "2H2 ", { 1.135, -.51, .89}, {0,0,0},
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/*7*/H, "3H2 ", { 1.135, -.51,-.89}, {0,0,0},
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EndOfList};
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static struct {int type; int atoms[2];} bonds[] =
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{CC,0,1,
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CH,0,2,CH,0,3,CH,0,4, // C1 methyl
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CH,1,5,CH,1,6,CH,1,7, // C2 methyl
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EndOfList};
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static struct {int type; int atoms[3];} angles[] =
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{HCC,2,0,1,HCC,3,0,1,HCC,4,0,1, // C1 methyl
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HCH,2,0,3,HCH,2,0,4,HCH,3,0,4,
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HCC,5,1,0,HCC,6,1,0,HCC,7,1,0, // C2 methyl
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HCH,5,1,6,HCH,5,1,7,HCH,6,1,7,
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EndOfList};
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static struct {int type; int atoms[4];} torsions[] =
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{HCCH,2,0,1,5,HCCH,2,0,1,6,HCCH,2,0,1,7,
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HCCH,3,0,1,5,HCCH,3,0,1,6,HCCH,3,0,1,7,
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HCCH,4,0,1,5,HCCH,4,0,1,6,HCCH,4,0,1,7,
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EndOfList};
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// PDB FILE WRITER
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// Given state data, output a single frame (pdb "model") of the trajectory.
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static void
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myWritePDBFrame(int frameNum, double timeInPs, double energyInKcal,
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const MyAtomInfo atoms[])
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{
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// Write out in PDB format -- printf is so much more compact than formatted cout.
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printf("MODEL %d\n", frameNum);
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printf("REMARK 250 time=%.3f ps; energy=%.3f kcal/mole\n",
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timeInPs, energyInKcal);
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for (int n=0; atoms[n].type != EndOfList; ++n)
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printf("ATOM %5d %4s ETH 1 %8.3f%8.3f%8.3f 1.00 0.00\n",
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n+1, atoms[n].pdb,
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atoms[n].posInAng[0], atoms[n].posInAng[1], atoms[n].posInAng[2]);
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printf("ENDMDL\n");
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}
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// -----------------------------------------------------------------------------
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// INTERFACE TO OpenMM
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// -----------------------------------------------------------------------------
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// These four functions and an opaque structure are used to interface our main
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// program with OpenMM without the main program having any direct interaction
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// with the OpenMM API. This is a clean approach for interfacing with any MD
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// code, although the details of the interface routines will differ. This is
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// still just "locally written" code and is not required by OpenMM.
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struct MyOpenMMData;
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static MyOpenMMData* myInitializeOpenMM(const MyAtomInfo atoms[],
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double stepSizeInFs,
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std::string& platformName);
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static void myStepWithOpenMM(MyOpenMMData*, int numSteps);
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static void myGetOpenMMState(MyOpenMMData*, bool wantEnergy,
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double& time, double& energy,
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MyAtomInfo atoms[]);
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static void myTerminateOpenMM(MyOpenMMData*);
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// -----------------------------------------------------------------------------
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// ETHANE MAIN PROGRAM
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// -----------------------------------------------------------------------------
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int main() {
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// ALWAYS enclose all OpenMM calls with a try/catch block to make sure that
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// usage and runtime errors are caught and reported.
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try {
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std::string platformName;
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// Set up OpenMM data structures; returns OpenMM Platform name.
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MyOpenMMData* omm = myInitializeOpenMM(atoms, StepSizeInFs, platformName);
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// Run the simulation:
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// (1) Write the first line of the PDB file and the initial configuration.
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// (2) Run silently entirely within OpenMM between reporting intervals.
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// (3) Write a PDB frame when the time comes.
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printf("REMARK Using OpenMM platform %s\n", platformName.c_str());
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const int NumSilentSteps = (int)(ReportIntervalInFs / StepSizeInFs + 0.5);
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for (int frame=1; ; ++frame) {
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double time, energy;
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myGetOpenMMState(omm, WantEnergy, time, energy, atoms);
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myWritePDBFrame(frame, time, energy, atoms);
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if (time >= SimulationTimeInPs)
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break;
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myStepWithOpenMM(omm, NumSilentSteps);
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}
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// Clean up OpenMM data structures.
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myTerminateOpenMM(omm);
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return 0; // Normal return from main.
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}
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// Catch and report usage and runtime errors detected by OpenMM and fail.
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catch(const std::exception& e) {
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printf("EXCEPTION: %s\n", e.what());
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return 1;
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}
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}
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// -----------------------------------------------------------------------------
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// OpenMM-USING CODE
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// -----------------------------------------------------------------------------
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// The OpenMM API is visible only at this point and below. Normally this would
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// be in a separate compilation module; we're including it here for simplicity.
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// -----------------------------------------------------------------------------
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// Suppress irrelevant warnings from Microsoft's compiler.
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#ifdef _MSC_VER
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#pragma warning(disable:4996) // sprintf is unsafe
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#endif
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#include "OpenMM.h"
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using OpenMM::Vec3; // so we can just say "Vec3" below
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// This is our opaque "handle" class containing all the OpenMM objects that
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// must persist from call to call during a simulation. The main program gets
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// a pointer to one of these but sees it as essentially a void* since it
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// doesn't know the definition of this class.
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struct MyOpenMMData {
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MyOpenMMData() : system(0), context(0), integrator(0) {}
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~MyOpenMMData() {delete context; delete integrator; delete system;}
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OpenMM::System* system;
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OpenMM::Integrator* integrator;
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OpenMM::Context* context;
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};
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// -----------------------------------------------------------------------------
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// INITIALIZE OpenMM DATA STRUCTURES
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// -----------------------------------------------------------------------------
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// We take these actions here:
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// (1) Load any available OpenMM plugins, e.g. Cuda and Brook.
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// (2) Allocate a MyOpenMMData structure to hang on to OpenMM data structures
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// in a manner which is opaque to the caller.
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// (3) Fill the OpenMM::System with the force field parameters we want to
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// use and the particular set of atoms to be simulated.
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// (4) Create an Integrator and a Context associating the Integrator with
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// the System.
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// (5) Select the OpenMM platform to be used.
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// (6) Return the MyOpenMMData struct and the name of the Platform in use.
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//
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// Note that this function must understand the calling MD code's molecule and
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// force field data structures so will need to be customized for each MD code.
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static MyOpenMMData*
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myInitializeOpenMM( const MyAtomInfo atoms[],
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double stepSizeInFs,
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std::string& platformName)
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{
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// Load all available OpenMM plugins from their default location.
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OpenMM::Platform::loadPluginsFromDirectory
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(OpenMM::Platform::getDefaultPluginsDirectory());
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// Allocate space to hold OpenMM objects while we're using them.
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MyOpenMMData* omm = new MyOpenMMData();
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// Create a System and Force objects within the System. Retain a reference
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// to each force object so we can fill in the forces. Note: the System owns
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// the force objects and will take care of deleting them; don't do it yourself!
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OpenMM::System& system = *(omm->system = new OpenMM::System());
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OpenMM::NonbondedForce& nonbond = *new OpenMM::NonbondedForce();
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OpenMM::HarmonicBondForce& bondStretch = *new OpenMM::HarmonicBondForce();
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OpenMM::HarmonicAngleForce& bondBend = *new OpenMM::HarmonicAngleForce();
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OpenMM::PeriodicTorsionForce& bondTorsion = *new OpenMM::PeriodicTorsionForce();
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system.addForce(&nonbond);
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system.addForce(&bondStretch);
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system.addForce(&bondBend);
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system.addForce(&bondTorsion);
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// Specify the atoms and their properties:
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// (1) System needs to know the masses.
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// (2) NonbondedForce needs charges,van der Waals properties (in MD units!).
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// (3) Collect default positions for initializing the simulation later.
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std::vector<Vec3> initialPosInNm;
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for (int n=0; atoms[n].type != EndOfList; ++n) {
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const AtomType& atype = atomType[atoms[n].type];
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system.addParticle(atype.mass);
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nonbond.addParticle(atype.charge,
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atype.vdwRadiusInAngstroms * OpenMM::NmPerAngstrom
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* OpenMM::SigmaPerVdwRadius,
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atype.vdwEnergyInKcal * OpenMM::KJPerKcal);
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// Convert the initial position to nm and append to the array.
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const Vec3 posInNm(atoms[n].initPosInAng[0] * OpenMM::NmPerAngstrom,
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atoms[n].initPosInAng[1] * OpenMM::NmPerAngstrom,
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atoms[n].initPosInAng[2] * OpenMM::NmPerAngstrom);
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initialPosInNm.push_back(posInNm);
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}
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// Process the bonds:
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// (1) If we're using constraints, tell System about constrainable bonds;
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// otherwise, tell HarmonicBondForce the bond stretch parameters
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// (tricky units!).
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// (2) Create a list of bonds for generating nonbond exclusions.
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std::vector< std::pair<int,int> > bondPairs;
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for (int i=0; bonds[i].type != EndOfList; ++i) {
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const int* atom = bonds[i].atoms;
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const BondType& bond = bondType[bonds[i].type];
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if (UseConstraints && bond.canConstrain) {
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system.addConstraint(atom[0], atom[1],
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bond.nominalLengthInAngstroms * OpenMM::NmPerAngstrom);
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} else {
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// Note factor of 2 for stiffness below because Amber specifies the constant
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// as it is used in the harmonic energy term kx^2 with force 2kx; OpenMM wants
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// it as used in the force term kx, with energy kx^2/2.
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bondStretch.addBond(atom[0], atom[1],
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bond.nominalLengthInAngstroms
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* OpenMM::NmPerAngstrom,
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bond.stiffnessInKcalPerAngstrom2
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* 2 * OpenMM::KJPerKcal
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* OpenMM::AngstromsPerNm * OpenMM::AngstromsPerNm);
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}
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bondPairs.push_back(std::make_pair(atom[0], atom[1]));
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}
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// Exclude 1-2, 1-3 bonded atoms from nonbonded forces, and scale down 1-4 bonded atoms.
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nonbond.createExceptionsFromBonds(bondPairs, Coulomb14Scale, LennardJones14Scale);
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// Create the 1-2-3 bond angle harmonic terms.
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for (int i=0; angles[i].type != EndOfList; ++i) {
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const int* atom = angles[i].atoms;
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const AngleType& angle = angleType[angles[i].type];
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// See note under bond stretch above regarding the factor of 2 here.
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bondBend.addAngle(atom[0],atom[1],atom[2],
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angle.nominalAngleInDegrees * OpenMM::RadiansPerDegree,
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angle.stiffnessInKcalPerRadian2 * 2 * OpenMM::KJPerKcal);
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}
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// Create the 1-2-3-4 bond torsion (dihedral) terms.
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for (int i=0; torsions[i].type != EndOfList; ++i) {
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const int* atom = torsions[i].atoms;
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const TorsionType& torsion = torsionType[torsions[i].type];
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bondTorsion.addTorsion(atom[0],atom[1],atom[2],atom[3],
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torsion.periodicity,
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torsion.phaseInDegrees * OpenMM::RadiansPerDegree,
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torsion.amplitudeInKcal * OpenMM::KJPerKcal);
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}
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// Choose an Integrator for advancing time, and a Context connecting the
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// System with the Integrator for simulation. Let the Context choose the
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// best available Platform. Initialize the configuration from the default
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// positions we collected above. Initial velocities will be zero.
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omm->integrator = new OpenMM::VerletIntegrator(StepSizeInFs * OpenMM::PsPerFs);
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omm->context = new OpenMM::Context(*omm->system, *omm->integrator);
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omm->context->setPositions(initialPosInNm);
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platformName = omm->context->getPlatform().getName();
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return omm;
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}
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// -----------------------------------------------------------------------------
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// COPY STATE BACK TO CPU FROM OPENMM
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// -----------------------------------------------------------------------------
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static void
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myGetOpenMMState(MyOpenMMData* omm, bool wantEnergy,
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double& timeInPs, double& energyInKcal,
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MyAtomInfo atoms[])
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{
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int infoMask = 0;
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infoMask = OpenMM::State::Positions;
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if (wantEnergy) {
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infoMask += OpenMM::State::Velocities; // for kinetic energy (cheap)
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infoMask += OpenMM::State::Energy; // for pot. energy (expensive)
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}
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// Forces are also available (and cheap).
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const OpenMM::State state = omm->context->getState(infoMask);
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timeInPs = state.getTime(); // OpenMM time is in ps already
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// Copy OpenMM positions into atoms array and change units from nm to Angstroms.
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const std::vector<Vec3>& positionsInNm = state.getPositions();
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for (int i=0; i < (int)positionsInNm.size(); ++i)
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for (int j=0; j < 3; ++j)
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atoms[i].posInAng[j] = positionsInNm[i][j] * OpenMM::AngstromsPerNm;
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// If energy has been requested, obtain it and convert from kJ to kcal.
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energyInKcal = 0;
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if (wantEnergy)
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energyInKcal = (state.getPotentialEnergy() + state.getKineticEnergy())
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* OpenMM::KcalPerKJ;
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}
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// -----------------------------------------------------------------------------
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// TAKE MULTIPLE STEPS USING OpenMM
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// -----------------------------------------------------------------------------
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static void
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myStepWithOpenMM(MyOpenMMData* omm, int numSteps) {
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omm->integrator->step(numSteps);
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}
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// -----------------------------------------------------------------------------
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// DEALLOCATE OpenMM OBJECTS
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// -----------------------------------------------------------------------------
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static void
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myTerminateOpenMM(MyOpenMMData* omm) {
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delete omm;
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}
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