// -----------------------------------------------------------------------------
// 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;
}
void writeTimeSeries(int steps, const OpenMM::State& state, std::ofstream &ots, double qscore) {
ots << std::setw(8) << steps;
ots << ' ' << std::fixed << std::setw(8) << std::setprecision(3) << qscore;
ots << ' ' << std::fixed << std::setw(8) << state.getPotentialEnergy();
ots << ' ' << std::fixed << std::setw(8) << state.getKineticEnergy();
ots << '\n';
}
// -----------------------------------------------------------------------------
// 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();
}
void simulate(json &molinfo) {
// Load any shared libraries containing GPU implementations.
OpenMM::Platform::loadPluginsFromDirectory(
OpenMM::Platform::getDefaultPluginsDirectory());
// force to use CPU platform that is better than CUDA in my simulation scale
OpenMM::Platform& platform = OpenMM::Platform::getPlatformByName("CPU");
// force to use single thread
platform.setPropertyDefaultValue("Threads", "1");
// Create a system with forces.
OpenMM::System system;
const int N_particles = molinfo["resSeq"].size();
std::cout << "# Number of Particles : " << N_particles << '\n';
// set MD paramters
const double Temperature = molinfo["parameters"]["Temperature"];
const int SimulationSteps = molinfo["parameters"]["SimulationSteps"];
const double TimePerStepInPs = molinfo["parameters"]["TimePerStepInPs"];
const int NStepSave = molinfo["parameters"]["NStepSave"];
const int RandomSeed = molinfo["parameters"]["RandomSeed"];
// set other parameters
const std::string filename = molinfo["output"]["filename"];
// Create Atoms
std::vector<OpenMM::Vec3> initPosInNm(N_particles);
// map from resSeq to particle index(0..N-1)
for (int i=0; i<N_particles; ++i) {
int resSeq = molinfo["resSeq"][i];
rs2pi.insert(std::pair<int,int>(resSeq, i));
}
double x, y, z;
for (int i=0; i<N_particles; ++i) {
x = molinfo["position"][i]["position"][0];
y = molinfo["position"][i]["position"][1];
z = molinfo["position"][i]["position"][2];
initPosInNm[i] = OpenMM::Vec3(x, y, z) * OpenMM::NmPerAngstrom;
system.addParticle(137.0); // average mass of amino acid residues
}
// add non-local repulsive force
// This pair potential is excluded from bonded pairs
OpenMM::CustomNonbondedForce& nonlocalRepulsion = *new OpenMM::CustomNonbondedForce("epsilon_repul*(d_exclusive/r)^12");
system.addForce(&nonlocalRepulsion);
nonlocalRepulsion.setNonbondedMethod(OpenMM::CustomNonbondedForce::NonbondedMethod::CutoffNonPeriodic);
nonlocalRepulsion.setCutoffDistance(D_ExclusionCutoffInNm);
nonlocalRepulsion.addGlobalParameter("d_exclusive", D_ExclusiveInNm);
nonlocalRepulsion.addGlobalParameter("epsilon_repul", E_ExclusionPair);
for (int i=0; i<N_particles; ++i) {
nonlocalRepulsion.addParticle();
}
// add non-local Go contact for native contact pairs
OpenMM::CustomBondForce& goContactForce = *new OpenMM::CustomBondForce("epsilon_ngo*(5*(r_native/r)^12 - 6*(r_native/r)^10)");
system.addForce(&goContactForce);
goContactForce.addGlobalParameter("epsilon_ngo", E_GoContactPair);
goContactForce.addPerBondParameter("r_native");
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"];
std::vector<double> perBondParams = {r_native * OpenMM::NmPerAngstrom};
goContactForce.addBond(p1, p2, perBondParams);
nonlocalRepulsion.addExclusion(p1, p2);
}
// add bonding force or constraints between two particles
OpenMM::HarmonicBondForce& bondStretch = *new OpenMM::HarmonicBondForce();
system.addForce(&bondStretch);
for (int i=0; i<molinfo["bond"].size(); ++i) {
int p1 = rs2pi[molinfo["bond"][i]["resSeq"][0]];
int p2 = rs2pi[molinfo["bond"][i]["resSeq"][1]];
double length = molinfo["bond"][i]["length"];
if (UseConstraints) {
system.addConstraint(p1, p2, length * OpenMM::NmPerAngstrom);
} else {
bondStretch.addBond(p1, p2, length * OpenMM::NmPerAngstrom, K_BondStretch);
}
nonlocalRepulsion.addExclusion(p1, p2);
}
// add angle force
OpenMM::HarmonicAngleForce& bondBend = *new OpenMM::HarmonicAngleForce();
system.addForce(&bondBend);
for (int i=0; i<molinfo["angle"].size(); ++i) {
int p1 = rs2pi[molinfo["angle"][i]["resSeq"][0]];
int p2 = rs2pi[molinfo["angle"][i]["resSeq"][1]];
int p3 = rs2pi[molinfo["angle"][i]["resSeq"][2]];
double angle = molinfo["angle"][i]["angle"];
bondBend.addAngle(p1, p2, p3, angle * OpenMM::RadiansPerDegree, K_BondAngle);
nonlocalRepulsion.addExclusion(p1, p3);
}
// add dihedral force
OpenMM::PeriodicTorsionForce& bondTorsion = *new OpenMM::PeriodicTorsionForce();
system.addForce(&bondTorsion);
for (int i=0; i<molinfo["dihedral"].size(); ++i) {
int p1 = rs2pi[molinfo["dihedral"][i]["resSeq"][0]];
int p2 = rs2pi[molinfo["dihedral"][i]["resSeq"][1]];
int p3 = rs2pi[molinfo["dihedral"][i]["resSeq"][2]];
int p4 = rs2pi[molinfo["dihedral"][i]["resSeq"][3]];
double dihedral = molinfo["dihedral"][i]["dihedral"];
bondTorsion.addTorsion(p1, p2, p3, p4,
1, (dihedral+180.0) * OpenMM::RadiansPerDegree, K_BondTorsion1);
bondTorsion.addTorsion(p1, p2, p3, p4,
3, (dihedral+180.0) * OpenMM::RadiansPerDegree, K_BondTorsion3);
nonlocalRepulsion.addExclusion(p1, p4);
}
// set langevin integrator
OpenMM::LangevinIntegrator integrator(Temperature, LangevinFrictionPerPs, TimePerStepInPs);
integrator.setRandomNumberSeed(RandomSeed);
// Let OpenMM Context choose best platform
OpenMM::Context context(system, integrator, platform);
std::cout << "# Using OpenMM Platform: ";
std::cout << context.getPlatform().getName().c_str() << std::endl;
// Set starting positions of the atoms. Leave time and velocity zero.
context.setPositions(initPosInNm);
// set initial velocity
context.setVelocitiesToTemperature(Temperature, RandomSeed);
// set output files
std::ofstream opdb, ots;
opdb.open(filename + ".pdb", std::ios::out);
ots.open(filename + ".ts", std::ios::out);
std::cout << "# PDB: " << filename + ".pdb\n";
std::cout << "# TimeSereis: " << filename + ".ts\n";
int infoMask = 0;
infoMask = OpenMM::State::Positions;
infoMask += OpenMM::State::Energy;
for (int frameNum = 0;; ++frameNum) {
// Output current state information
OpenMM::State state = context.getState(infoMask);
int steps = frameNum * NStepSave;
double qscore = getQscore(state, molinfo);
// write PDB frame
writePDBFrame(frameNum, state, molinfo, opdb);
writeTimeSeries(steps, state, ots, qscore);
// show progress in stdout
if (SilentMode == false) {
std::cout << '\r';
std::cout << "Q=" << std::setw(5) << std::setprecision(3) << qscore;
std::cout << "; T=" << std::setw(5) << integrator.getTemperature();
std::cout << "; E=" << std::setw(5) << state.getPotentialEnergy();
std::cout << std::setw(8) << steps << " steps / ";
std::cout << std::setw(8) << SimulationSteps << std::flush;
}
if (frameNum * NStepSave >= SimulationSteps) break;
integrator.step(NStepSave);
}
std::cout << std::endl;
opdb.close();
ots.close();
}
