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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
int main() {
Biotype::initializePopularBiotypes();
AminoAcidResidue::Alanine alanine1, alanine2;
alanine1.assignBiotypes();
alanine2.assignBiotypes();
AminoAcidResidue::Serine serine1, serine2;
serine1.assignBiotypes();
serine2.assignBiotypes();
CompoundSystem system;
SimbodyMatterSubsystem matter(system);
// DecorationSubsystem decorations(system);
DuMMForceFieldSubsystem dumm(system);
GeneralForceSubsystem forces(system);
// ifstream tinkerStream("../../resources/tinker_amber99_clean.prm");
// dumm.populateFromTinkerParameterFile(tinkerStream);
// tinkerStream.close();
dumm.loadAmber99Parameters();
// system.adoptCompound(alanine1);
// system.adoptCompound(alanine2);
// system.adoptCompound(serine1);
// system.adoptCompound(serine2);
DuMM::ChargedAtomTypeIndex ethaneCType(4000);
dumm.defineChargedAtomType(ethaneCType, "ethane C", DuMM::AtomClassIndex(1), -0.075);
dumm.setBiotypeChargedAtomType(ethaneCType, Biotype::get("ethane", "C").getIndex());
DuMM::ChargedAtomTypeIndex ethaneHType(4001);
dumm.defineChargedAtomType(ethaneHType, "ethane C", DuMM::AtomClassIndex(35), 0.025);
dumm.setBiotypeChargedAtomType(ethaneHType, Biotype::get("ethane", "H").getIndex());
Ethane ethane1, ethane2;
// system.adoptCompound(ethane1);
// system.adoptCompound(ethane2);
// Protein protein("ACDEFGHIKLMNPQRSTVWY");
Protein protein("AAAAAAAAAA");
// Protein protein("APF");
protein.assignBiotypes();
system.adoptCompound( protein, Vec3(1.5, 0, 0) );
DuMM::AtomClassIndex argonClass(200);
dumm.defineAtomClass_KA(argonClass, "argon", 18, 0, 1.88, 0.2);
DuMM::ChargedAtomTypeIndex argonType(4010);
dumm.defineChargedAtomType(argonType, "argon", argonClass, 0.0);
dumm.setBiotypeChargedAtomType(argonType, Biotype::get("argon", "argon").getIndex());
Argon argon1, argon2;
// system.adoptCompound( argon1 );
// system.adoptCompound( argon2, Vec3(0.7, 0, 0) );
system.modelCompounds();
Force::GlobalDamper(forces, matter, 0.1);
State state = system.realizeTopology();
#ifdef CREATE_VIZ_WINDOW
Visualizer display(system, 0.1);
#endif
RungeKuttaMersonIntegrator study(system);
// CPodesIntegrator study(system, CPodes::BDF, CPodes::Newton);
study.setAccuracy(1e-2);
state.updU() = 1.;
state.updU()(0,6) = 0; // no rigid body motion
study.initialize(state);
#ifdef CREATE_VIZ_WINDOW
display.report(study.getState());
#endif
Real timeInterval = 0.05;
for (Real time=0.0; time < (10 * timeInterval); time += timeInterval) // picoseconds
{
study.stepTo(time);
#ifdef CREATE_VIZ_WINDOW
display.report(study.getState());
#endif
}
}
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