OpenMM::System* AmberParm::createSystem(
OpenMM::NonbondedForce::NonbondedMethod nonbondedMethod,
double nonbondedCutoff,
std::string constraints,
bool rigidWater,
std::string implicitSolvent,
double implicitSolventKappa,
double implicitSolventSaltConc,
double temperature,
double soluteDielectric,
double solventDielectric,
bool removeCMMotion,
double ewaldErrorTolerance,
bool flexibleConstraints,
bool useSASA) {
OpenMM::System* system = new OpenMM::System();
// Make sure we have a legal choice for constraints and implicitSolvent
if (constraints != "None" && constraints != "HBonds" &&
constraints != "AllBonds") {
string msg = "constraints must be None, HBonds, or AllBonds; not " +
constraints;
throw AmberParmError(msg.c_str());
}
if (implicitSolvent != "None" && implicitSolvent != "HCT" &&
implicitSolvent != "OBC1" && implicitSolvent != "OBC2" &&
implicitSolvent != "GBn" && implicitSolvent != "GBn2") {
string msg = "implicitSolvent must be None, HCT, OBC1, OBC2, GBn, or "
"GBn2; not " + implicitSolvent;
throw AmberParmError(msg.c_str());
}
if (rigidWater && (constraints != "HBonds" && constraints != "AllBonds")) {
cerr << "rigidWater is incompatible with constraints=None; setting to "
<< "false" << endl;
}
// Catch illegal nonbonded choice for system
if (isPeriodic()) {
if (nonbondedMethod == OpenMM::NonbondedForce::CutoffNonPeriodic ||
nonbondedMethod == OpenMM::NonbondedForce::NoCutoff)
throw AmberParmError("Illegal nonbondedForce choice for periodic system");
} else {
if (nonbondedMethod == OpenMM::NonbondedForce::CutoffPeriodic ||
nonbondedMethod == OpenMM::NonbondedForce::PME ||
nonbondedMethod == OpenMM::NonbondedForce::Ewald)
throw AmberParmError("Illegal nonbondedForce choice for non-periodic system");
}
// Add all particles
for (atom_iterator it = AtomBegin(); it != AtomEnd(); it++) {
system->addParticle(it->getMass());
}
// Add constraints
bool hcons = constraints == "HBonds" || constraints == "AllBonds";
bool allcons = constraints == "AllBonds";
for (bond_iterator it = BondBegin(); it != BondEnd(); it++) {
Atom a1 = atoms_[it->getAtomI()];
Atom a2 = atoms_[it->getAtomJ()];
if (hcons && (a1.getElement() == 1 || a2.getElement() == 1)) {
system->addConstraint(it->getAtomI(), it->getAtomJ(),
it->getEquilibriumDistance()*NANOMETER_PER_ANGSTROM);
} else if (allcons) {
system->addConstraint(it->getAtomI(), it->getAtomJ(),
it->getEquilibriumDistance()*NANOMETER_PER_ANGSTROM);
}
}
// Add all bonds
if (!allcons || flexibleConstraints) {
OpenMM::HarmonicBondForce *bond_force = new OpenMM::HarmonicBondForce();
bond_force->setForceGroup(BOND_FORCE_GROUP);
double conv = ANGSTROM_PER_NANOMETER*ANGSTROM_PER_NANOMETER*JOULE_PER_CALORIE;
for (bond_iterator it=BondBegin(); it != BondEnd(); it++) {
// See if this bond needs to be skipped due to constraints
Atom a1 = atoms_[it->getAtomI()];
Atom a2 = atoms_[it->getAtomJ()];
if (hcons && (a1.getElement() == 1 || a2.getElement() == 1) &&
!flexibleConstraints) continue;
bond_force->addBond(it->getAtomI(), it->getAtomJ(),
it->getEquilibriumDistance()*NANOMETER_PER_ANGSTROM,
2*it->getForceConstant()*conv);
}
system->addForce(bond_force);
}
// Add all angles
OpenMM::HarmonicAngleForce *angle_force = new OpenMM::HarmonicAngleForce();
angle_force->setForceGroup(ANGLE_FORCE_GROUP);
for (angle_iterator it = AngleBegin(); it != AngleEnd(); it++) {
angle_force->addAngle(it->getAtomI(), it->getAtomJ(), it->getAtomK(),
it->getEquilibriumAngle()*RADIAN_PER_DEGREE,
2*it->getForceConstant()*JOULE_PER_CALORIE);
}
system->addForce(angle_force);
// Add all torsions
OpenMM::PeriodicTorsionForce *dihedral_force = new OpenMM::PeriodicTorsionForce();
dihedral_force->setForceGroup(DIHEDRAL_FORCE_GROUP);
for (dihedral_iterator it = DihedralBegin(); it != DihedralEnd(); it++) {
dihedral_force->addTorsion(it->getAtomI(), it->getAtomJ(),
it->getAtomK(), it->getAtomL(),
it->getPeriodicity(),
it->getPhase()*RADIAN_PER_DEGREE,
it->getForceConstant()*JOULE_PER_CALORIE);
}
system->addForce(dihedral_force);
// Add nonbonded force
OpenMM::NonbondedForce *nonb_frc = new OpenMM::NonbondedForce();
nonb_frc->setForceGroup(NONBONDED_FORCE_GROUP);
nonb_frc->setNonbondedMethod(nonbondedMethod);
if (nonbondedMethod != OpenMM::NonbondedForce::NoCutoff)
nonb_frc->setCutoffDistance(nonbondedCutoff*NANOMETER_PER_ANGSTROM);
const double ONE_SIXTH = 1.0 / 6.0;
const double SIGMA_SCALE = pow(2, -ONE_SIXTH) * 2 * NANOMETER_PER_ANGSTROM;
for (atom_iterator it = AtomBegin(); it != AtomEnd(); it++) {
nonb_frc->addParticle(it->getCharge(),
it->getLJRadius()*SIGMA_SCALE,
it->getLJEpsilon()*JOULE_PER_CALORIE);
}
// Now do exceptions
const double SIGMA_SCALE2 = pow(2, -ONE_SIXTH) * NANOMETER_PER_ANGSTROM;
for (dihedral_iterator it = DihedralBegin(); it != DihedralEnd(); it++) {
if (it->ignoreEndGroups()) continue;
Atom a1 = atoms_[it->getAtomI()];
Atom a2 = atoms_[it->getAtomL()];
double eps = sqrt(a1.getLJEpsilon() * a2.getLJEpsilon()) *
JOULE_PER_CALORIE / it->getScnb();
double sig = (a1.getLJRadius() + a2.getLJRadius()) * SIGMA_SCALE2;
nonb_frc->addException(it->getAtomI(), it->getAtomL(),
a1.getCharge()*a2.getCharge()/it->getScee(),
sig, eps);
}
// Now do exclusions
for (int i = 0; i < atoms_.size(); i++) {
if (exclusion_list_[i].size() == 0) continue; // No exclusions here
for (set<int>::const_iterator it = exclusion_list_[i].begin();
it != exclusion_list_[i].end(); it++) {
nonb_frc->addException(i, *it, 0.0, 1.0, 0.0);
}
}
// Set the ewald error tolerance
if (nonbondedMethod == OpenMM::NonbondedForce::PME ||
nonbondedMethod == OpenMM::NonbondedForce::Ewald)
nonb_frc->setEwaldErrorTolerance(ewaldErrorTolerance);
system->addForce(nonb_frc);
// See about removing the center of mass motion
if (removeCMMotion)
system->addForce(new OpenMM::CMMotionRemover());
// Add a box if necessary
if (isPeriodic())
system->setDefaultPeriodicBoxVectors(unit_cell_.getVectorA()/10,
unit_cell_.getVectorB()/10,
unit_cell_.getVectorC()/10);
// If no implicit solvent, we can return system now
if (implicitSolvent == "None")
return system;
// Otherwise, we need to add the GB force
if (implicitSolventKappa <= 0 && implicitSolventSaltConc > 0)
implicitSolventKappa = 50.33355 * 0.73 *
sqrt(implicitSolventSaltConc/(solventDielectric*temperature));
OpenMM::CustomGBForce *gb_frc = 0;
if (implicitSolvent == "HCT") {
gb_frc = GB_HCT(*this, solventDielectric, soluteDielectric, useSASA,
nonbondedCutoff, implicitSolventKappa);
} else if (implicitSolvent == "OBC1") {
gb_frc = GB_OBC1(*this, solventDielectric, soluteDielectric, useSASA,
nonbondedCutoff, implicitSolventKappa);
} else if (implicitSolvent == "OBC2") {
gb_frc = GB_OBC2(*this, solventDielectric, soluteDielectric, useSASA,
nonbondedCutoff, implicitSolventKappa);
} else if (implicitSolvent == "GBn") {
gb_frc = GB_GBn(*this, solventDielectric, soluteDielectric, useSASA,
nonbondedCutoff, implicitSolventKappa);
} else if (implicitSolvent == "GBn2") {
gb_frc = GB_GBn2(*this, solventDielectric, soluteDielectric, useSASA,
nonbondedCutoff, implicitSolventKappa);
} else {
stringstream iss;
iss << "Should not be here; bad GB model " << implicitSolvent;
throw InternalError(iss.str());
}
if (nonbondedMethod == OpenMM::NonbondedForce::NoCutoff)
gb_frc->setNonbondedMethod(OpenMM::CustomGBForce::NoCutoff);
else if (nonbondedMethod == OpenMM::NonbondedForce::CutoffNonPeriodic)
gb_frc->setNonbondedMethod(OpenMM::CustomGBForce::CutoffNonPeriodic);
else // all remaining options are periodic cutoff...
gb_frc->setNonbondedMethod(OpenMM::CustomGBForce::CutoffPeriodic);
gb_frc->setForceGroup(NONBONDED_FORCE_GROUP);
// Since we're using GB, we need to turn off the reaction field dielectric
nonb_frc->setReactionFieldDielectric(1.0);
system->addForce(gb_frc);
return system;
}
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();
}