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/* -------------------------------------------------------------------------- *
* SimTK Core: SimTK Molmodel *
* -------------------------------------------------------------------------- *
* This is part of the SimTK Core biosimulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2006-7 Stanford University and the Authors. *
* Authors: Christopher Bruns *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "SimTKmolmodel.h"
#include <iostream>
#include <vector>
using std::cout;
using std::endl;
using namespace SimTK;
using namespace std;
// define CREATE_VIZ_WINDOW to see animated window of simulation
// undefine for automated nightly builds
// #define CREATE_VIZ_WINDOW
void testIssue907()
{
CompoundSystem system;
SimbodyMatterSubsystem matter(system);
GeneralForceSubsystem forces(system);
DuMMForceFieldSubsystem dumm(system);
dumm.loadAmber99Parameters();
dumm.setCoulombGlobalScaleFactor(0);//meterReader.globalCoulombScaleFactor);
dumm.setBondTorsionGlobalScaleFactor(1);//meterReader.globalBondTorsionScaleFactor);
dumm.setGbsaGlobalScaleFactor(0);//meterReader.globalGbsaScaleFactor);
dumm.setVdwGlobalScaleFactor(0);//meterReader.globalVdwScaleFactor);
dumm.setBondStretchGlobalScaleFactor(0);//meterReader.globalBondStretchScaleFactor);
dumm.setBondBendGlobalScaleFactor(0);//meterReader.globalBondBendScaleFactor);
dumm.setAmberImproperTorsionGlobalScaleFactor(0);//meterReader.globalAmberImproperTorsionScaleFactor);
Biopolymer myMolecule;
// myMolecule = Protein( "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"); //50 //ok
myMolecule = Protein("WWGGLLAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA");
// myMolecule.assignBiotypes();
system.adoptCompound(myMolecule,Vec3( 0,0,0));
cout<<"about to modelCompounds"<<endl;
time_t rawtime;
struct tm * timeinfo;
time ( &rawtime );
timeinfo = localtime ( &rawtime );
cout<<" time:"<< asctime (timeinfo) <<endl;
system.modelCompounds();
time ( &rawtime );
timeinfo = localtime ( &rawtime );
cout<<" time:"<< asctime (timeinfo) <<endl;
cout<<"done with modelCompounds"<<endl;
State state = system.realizeTopology();
system.realize(state,Stage::Position);
VerletIntegrator study(system,.002);
TimeStepper ts(system,study);
ts.initialize(state);
//# putting writeDefaultPdb here was fine to 2200 residues
cout <<"1 about to write default pdb coords to test.pdb"<<endl;
myMolecule.writeDefaultPdb("test.pdb",Vec3(0));
cout <<"1 just wrote default pdb coords to test.pdb"<<endl;
cout<<"[Repel.h:ConstrainedDynamics] Starting dynamics now."<<endl;
time ( &rawtime );
timeinfo = localtime ( &rawtime );
cout<<" time:"<< asctime (timeinfo) <<endl;
//cout <<"2 about to write default pdb coords to test.pdb"<<endl;
//myMolecule.writeDefaultPdb("test.pdb",Vec3(0));
//cout <<"2 just wrote default pdb coords to test.pdb"<<endl;
ts.stepTo(.1);
time ( &rawtime );
timeinfo = localtime ( &rawtime );
cout<<" time:"<< asctime (timeinfo) <<endl;
cout<<"done."<<endl;
}
void testShortProtein()
{
// Biotype::initializePopularBiotypes();
CompoundSystem system;
SimbodyMatterSubsystem matter(system);
DuMMForceFieldSubsystem dumm(system);
DecorationSubsystem decorations(system);
// ifstream tinkerStream("../../resources/tinker_amber99_clean.prm");
// dumm.populateFromTinkerParameterFile(tinkerStream);
// tinkerStream.close();
dumm.loadAmber99Parameters();
// Protein protein("ACDEFGHIKLMNPQRSTVWY");
Protein protein("SPFGR");
protein.assignBiotypes();
protein.writeDefaultPdb(cout);
system.adoptCompound(protein);
system.modelCompounds();
State state = system.realizeTopology();
#ifdef CREATE_VIZ_WINDOW
Visualizer viz(system);
system.addEventReporter( new Visualizer::Reporter(viz, 0.005) );
#endif
RungeKuttaMersonIntegrator study(system);
study.initialize(state);
int numberOfSteps = 3;
#ifdef CREATE_VIZ_WINDOW
numberOfSteps = 1000;
#endif
TimeStepper ts(system, study);
ts.initialize(state);
ts.stepTo(numberOfSteps * 0.0050);
}
int main() {
testShortProtein();
testIssue907();
}
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