Ejemplo n.º 1
0
// -----------------------------------------------------------------------------
//                     COPY STATE BACK TO CPU FROM OPENMM
// -----------------------------------------------------------------------------
static void
myGetOpenMMState(MyOpenMMData* omm, bool wantEnergy, 
                 double& timeInPs, double& energyInKcal,
                 MyAtomInfo atoms[])
{
    int infoMask = 0;
    infoMask = OpenMM::State::Positions;
    if (wantEnergy) {
        infoMask += OpenMM::State::Velocities; // for kinetic energy (cheap)
        infoMask += OpenMM::State::Energy;     // for pot. energy (expensive)
    }
    // Forces are also available (and cheap).

    const OpenMM::State state = omm->context->getState(infoMask);
    timeInPs = state.getTime(); // OpenMM time is in ps already

    // Copy OpenMM positions into atoms array and change units from nm to Angstroms.
    const std::vector<Vec3>& positionsInNm = state.getPositions();
    for (int i=0; i < (int)positionsInNm.size(); ++i)
        for (int j=0; j < 3; ++j)
            atoms[i].posInAng[j] = positionsInNm[i][j] * OpenMM::AngstromsPerNm;

    // If energy has been requested, obtain it and convert from kJ to kcal.
    energyInKcal = 0;
    if (wantEnergy) 
        energyInKcal = (state.getPotentialEnergy() + state.getKineticEnergy())
                        * OpenMM::KcalPerKJ;
}
Ejemplo n.º 2
0
// -----------------------------------------------------------------------------
//                     COPY STATE BACK TO CPU FROM OPENMM
// -----------------------------------------------------------------------------
static void
myGetOpenMMState(MyOpenMMData* omm, double& timeInPs,
                 std::vector<double>& atomPositionsInAng)
{
    const OpenMM::State state = omm->context->getState(OpenMM::State::Positions, true);
    timeInPs = state.getTime(); // OpenMM time is in ps already

    // Copy OpenMM positions into output array and change units from nm to Angstroms.
    const std::vector<Vec3>& positionsInNm = state.getPositions();
    atomPositionsInAng.resize(3*positionsInNm.size());
    for (int i=0; i < (int)positionsInNm.size(); ++i)
        for (int j=0; j < 3; ++j)
            atomPositionsInAng[3*i+j] = positionsInNm[i][j] * OpenMM::AngstromsPerNm;
}
Ejemplo n.º 3
0
double getQscore(const OpenMM::State& state, json &molinfo) {
	const std::vector<OpenMM::Vec3>& posInNm = state.getPositions();

	int contact = 0;
	for (int i=0; i<molinfo["contact"].size(); ++i) {
		int p1 = rs2pi[molinfo["contact"][i]["resSeq"][0]];
		int p2 = rs2pi[molinfo["contact"][i]["resSeq"][1]];
		double r_native = molinfo["contact"][i]["length"];
		double r, r2;
		r2  = pow(posInNm[p1][0]-posInNm[p2][0], 2);
		r2 += pow(posInNm[p1][1]-posInNm[p2][1], 2);
		r2 += pow(posInNm[p1][2]-posInNm[p2][2], 2);
		r = sqrt(r2) / OpenMM::NmPerAngstrom;
		if (r < r_native * QscoreThreshold ) contact++;
	}
	return ((double)contact) / molinfo["contact"].size();
}
Ejemplo n.º 4
0
void writePDBFrame(int frameNum, const OpenMM::State& state, json &molinfo, std::ofstream &opdb) {
	// Reference atomic positions in the OpenMM State.
	const std::vector<OpenMM::Vec3>& posInNm = state.getPositions();

	opdb << "MODEL " << frameNum << "\n";
	for (int a = 0; a < (int)posInNm.size(); ++a)
	{
		opdb << "ATOM  " << std::setw(5) << a+1 << "  C    C  A";
		opdb << std::setw(4) << (int)molinfo["resSeq"][a];
		opdb << "    "; // atom number
		opdb << std::fixed << std::setw(8) << std::setprecision(3) << posInNm[a][0]*10;
		opdb << std::fixed << std::setw(8) << std::setprecision(3) << posInNm[a][1]*10;
		opdb << std::fixed << std::setw(8) << std::setprecision(3) << posInNm[a][2]*10;
		opdb << "  1.00  0.00\n";
	}
	opdb << "ENDMDL\n"; // end of frame
}
Ejemplo n.º 5
0
void OpenMMIntegrator::run( int numTimesteps ) {
	preStepModify();
	
	bool execute = true;

/*#ifdef HAVE_OPENMM_LTMD
	if( mLTMDParameters.ShouldProtoMolDiagonalize && mLTMDParameters.ShouldForceRediagOnMinFail ){
		if( app->eigenInfo.OpenMMMinimize ){
			OpenMM::LTMD::Integrator *ltmd = dynamic_cast<OpenMM::LTMD::Integrator*>( integrator );
			
			bool minimizePassed = ltmd->minimize( 50, 2 );
			
			if( minimizePassed || app->eigenInfo.RediagonalizationCount >= 5 ){
				if( app->eigenInfo.RediagonalizationCount >= 5 ){
					std::cout << "Maximum Rediagonalizations Reached" << std::endl;
				}
				
				execute = true;
				app->eigenInfo.OpenMMMinimize = false;
				app->eigenInfo.RediagonalizationCount = 0;
				std::cout << "Exiting Rediagonalizations" << std::endl;
			}else{
				execute = false;
				app->eigenInfo.reDiagonalize = true;
				app->eigenInfo.RediagonalizationCount++;
			}
		}
	}
#endif */
	integrator->step( numTimesteps );

	// Retrive data
	const OpenMM::State state = context->getState( OpenMM::State::Positions |
								OpenMM::State::Velocities |
								OpenMM::State::Forces |
								OpenMM::State::Energy );
								
	const std::vector<OpenMM::Vec3> positions( state.getPositions() );
	const std::vector<OpenMM::Vec3> velocities( state.getVelocities() );
	const std::vector<OpenMM::Vec3> forces( state.getForces() );
	
	const unsigned int sz = app->positions.size();
	for( unsigned int i = 0; i < sz; ++i ) {
		for( int j = 0; j < 3; j++ ) {
			app->positions[i].c[j] = positions[i][j] * Constant::NM_ANGSTROM; //nm to A
			app->velocities[i].c[j] = velocities[i][j] * Constant::NM_ANGSTROM *
									  Constant::TIMEFACTOR * Constant::FS_PS; //nm/ps to A/fs?
			( *myForces )[i].c[j] = forces[i][j] * Constant::INV_NM_ANGSTROM * Constant::KJ_KCAL; //KJ/nm to Kcal/A
		}
	}

	app->energies.clear();
	
	//clear old energies
	app->energies[ScalarStructure::COULOMB] =
		app->energies[ScalarStructure::LENNARDJONES] =
			app->energies[ScalarStructure::BOND] =
				app->energies[ScalarStructure::ANGLE] =
					app->energies[ScalarStructure::DIHEDRAL] =
						app->energies[ScalarStructure::IMPROPER] = 0.0;

	//save total potential energy
	app->energies[ScalarStructure::OTHER] = state.getPotentialEnergy() * Constant::KJ_KCAL;

	//fix time as no forces calculated
	app->topology->time += numTimesteps * getTimestep();
	
	postStepModify();
}