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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()
{
CompoundSystem system;
SimbodyMatterSubsystem matter(system);
DecorationSubsystem decorations(system);
DuMMForceFieldSubsystem dumm(system);
dumm.loadAmber99Parameters();
RNA rna("GCAU");
rna.assignBiotypes();
system.adoptCompound(rna);
rna.writeDefaultPdb(cout);
RibonucleotideResidue::Cytidylate cytidylate;
cytidylate.assignBiotypes();
// system.adoptCompound(cytidylate);
Real desiredAngle = 200*Deg2Rad;
cout << "desired chi = " << DuMM::Rad2Deg * desiredAngle << endl;
cytidylate.setDefaultDihedralAngle("chi", desiredAngle);
cout << "default chi = " << DuMM::Rad2Deg * cytidylate.calcDefaultDihedralAngle("chi") << endl;
system.modelCompounds();
State state = system.realizeTopology();
#ifdef CREATE_VIZ_WINDOW
Visualizer display(system);
#endif
RungeKuttaMersonIntegrator study(system);
study.initialize(state);
#ifdef CREATE_VIZ_WINDOW
display.report(study.getState());
#endif
Real timeInterval = 0.0020; // picoseconds
for (Real time=0.0; time < 10 * timeInterval; time += timeInterval) { // picoseconds
study.stepTo(time);
rna.writePdb(study.getState(), cout);
#ifdef CREATE_VIZ_WINDOW
display.report(study.getState());
#endif
// cout << "state chi1 = " << DuMM::Rad2Deg * cytidylate.getDihedralAngle(study.getState(), "chi1") << endl;
// cout << "default chi1 = " << DuMM::Rad2Deg * cytidylate.getDefaultDihedralAngle("chi1") << endl;
}
}
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