// -----------------------------------------------------------------------------
// 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;
}
// -----------------------------------------------------------------------------
// 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;
}
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();
}
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
}
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();
}