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/* -------------------------------------------------------------------------- *
* SimTK Molmodel Example: Simple RNA *
* -------------------------------------------------------------------------- *
* This is the second example from the Molmodel User's Guide. It creates a *
* small RNA molecule, simulates it, generates a live animation while it is *
* running and generates a multi-frame pdb file to look at later. *
* *
* Authors: Christopher Bruns, Michael Sherman *
* -------------------------------------------------------------------------- */
#include "Molmodel.h"
#include <iostream>
#include <fstream>
#include <exception>
using namespace SimTK;
// We'll create a file of this name in the current working directory.
const char* PdbFileName = "simpleRNA.pdb";
int main() {
try {
// molecule-specialized Simbody System
CompoundSystem system;
SimbodyMatterSubsystem matter(system);
GeneralForceSubsystem forces(system); // for Nose-Hoover
DecorationSubsystem decorations(system);
// molecular force field
DuMMForceFieldSubsystem forceField(system);
forceField.loadAmber99Parameters();
// This is adenine-uracil-guanine.
RNA rna("AUG");
rna.assignBiotypes();
system.adoptCompound(rna);
// Use a Nose-Hoover thermostat, which is a continuous force element
// rather than a periodic discontinuous "disturbance" like the
// VelocityRescalingThermostat. We're using the default relaxation time.
NoseHooverThermostat thermo(forces, matter, 293.15);
// Show me a movie with a frame every 20fs.
system.addEventReporter(new Visualizer::Reporter(system, 0.020) );
// Generate a pdb file with a frame every 100fs.
std::ofstream pdbFile; pdbFile.open(PdbFileName);
system.addEventReporter(new PeriodicPdbWriter(system, pdbFile, 0.100));
// finalize multibody system
system.modelCompounds();
// Instantiate simbody model
system.realizeTopology();
State state = system.getDefaultState();
// Relax the structure before dynamics run
LocalEnergyMinimizer::minimizeEnergy(system, state, 15.0);
// Simulate it.
VerletIntegrator integ(system);
TimeStepper ts(system, integ);
ts.initialize(state);
ts.stepTo(10.0); // 10 ps
pdbFile.close();
std::cout << "\nWrote pdb file "
<< Pathname::getCurrentWorkingDirectory() << PdbFileName << "\n";
return 0;
}
catch(const std::exception& e) {
std::cerr << "ERROR: " << e.what() << std::endl;
return 1;
}
catch(...) {
std::cerr << "ERROR: An unknown exception was raised" << std::endl;
return 1;
}
}
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