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// -----------------------------------------------------------------------------
// OpenMM(tm) HelloArgon example in C++ (June 2009)
// -----------------------------------------------------------------------------
// This program demonstrates a simple molecular simulation using the OpenMM
// API for GPU-accelerated molecular dynamics simulation. The primary goal is
// to make sure you can compile, link, and run with OpenMM and view the output.
// The example is available in C++, C, and Fortran 95.
//
// The system modeled here is a small number of argon atoms in a vacuum.
// A multi-frame PDB file is written to stdout which can be read by VMD or
// other visualization tool to produce an animation of the resulting trajectory.
// -----------------------------------------------------------------------------
#include "OpenMM.h"
#include <cstdio>
// Forward declaration of routine for printing one frame of the
// trajectory, defined later in this source file.
void writePdbFrame(int frameNum, const OpenMM::State&);
void simulateArgon()
{
// Load any shared libraries containing GPU implementations.
OpenMM::Platform::loadPluginsFromDirectory(
OpenMM::Platform::getDefaultPluginsDirectory());
// Create a system with nonbonded forces.
OpenMM::System system;
OpenMM::NonbondedForce* nonbond = new OpenMM::NonbondedForce();
system.addForce(nonbond);
// Create three atoms.
std::vector<OpenMM::Vec3> initPosInNm(3);
for (int a = 0; a < 3; ++a)
{
initPosInNm[a] = OpenMM::Vec3(0.5*a,0,0); // location, nm
system.addParticle(39.95); // mass of Ar, grams per mole
// charge, L-J sigma (nm), well depth (kJ)
nonbond->addParticle(0.0, 0.3350, 0.996); // vdWRad(Ar)=.188 nm
}
OpenMM::VerletIntegrator integrator(0.004); // step size in ps
// Let OpenMM Context choose best platform.
OpenMM::Context context(system, integrator);
printf( "REMARK Using OpenMM platform %s\n",
context.getPlatform().getName().c_str() );
// Set starting positions of the atoms. Leave time and velocity zero.
context.setPositions(initPosInNm);
// Simulate.
for (int frameNum=1; ;++frameNum) {
// Output current state information.
OpenMM::State state = context.getState(OpenMM::State::Positions);
const double timeInPs = state.getTime();
writePdbFrame(frameNum, state); // output coordinates
if (timeInPs >= 10.)
break;
// Advance state many steps at a time, for efficient use of OpenMM.
integrator.step(10); // (use a lot more than this normally)
}
}
int main()
{
try {
simulateArgon();
return 0; // success!
}
// Catch and report usage and runtime errors detected by OpenMM and fail.
catch(const std::exception& e) {
printf("EXCEPTION: %s\n", e.what());
return 1; // failure!
}
}
// Handy homebrew PDB writer for quick-and-dirty trajectory output.
void writePdbFrame(int frameNum, const OpenMM::State& state)
{
// Reference atomic positions in the OpenMM State.
const std::vector<OpenMM::Vec3>& posInNm = state.getPositions();
// Use PDB MODEL cards to number trajectory frames
printf("MODEL %d\n", frameNum); // start of frame
for (int a = 0; a < (int)posInNm.size(); ++a)
{
printf("ATOM %5d AR AR 1 ", a+1); // atom number
printf("%8.3f%8.3f%8.3f 1.00 0.00\n", // coordinates
// "*10" converts nanometers to Angstroms
posInNm[a][0]*10, posInNm[a][1]*10, posInNm[a][2]*10);
}
printf("ENDMDL\n"); // end of frame
}
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