1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
|
/* -------------------------------------------------------------------------- *
* SimTK Molmodel Example: Simple Protein *
* -------------------------------------------------------------------------- *
* This is the first example from the Molmodel User's Guide. It creates a *
* small protein (a five-residue peptide), simulates it and generates a live *
* animation while it is running. *
* *
* Authors: Christopher Bruns, Michael Sherman *
* -------------------------------------------------------------------------- */
#include "Molmodel.h"
#include <iostream>
#include <exception>
using namespace SimTK;
int main() {
try {
// molecule-specialized simbody System
CompoundSystem system;
SimbodyMatterSubsystem matter(system);
DecorationSubsystem decorations(system);
// molecular force field
DuMMForceFieldSubsystem forceField(system);
forceField.loadAmber99Parameters();
// Create a five-residue protein. Neutral end caps are automatically
// added unless you suppress them. This is
// (Ace-) Ser-Ile-Met-Thr-Lys (-Nac).
Protein protein("SIMTK");
protein.assignBiotypes();
system.adoptCompound(protein);
// finalize mapping of atoms to bodies
system.modelCompounds();
// show me a movie
system.addEventReporter(new Visualizer::Reporter(system, 0.020));
// Maintain a constant temperature. (This isn't a very good
// thermostat -- consider NoseHooverThermostat instead.)
system.addEventHandler(new VelocityRescalingThermostat(
system, 293.15, 0.1));
// Instantiate simbody model and get default state
State state = system.realizeTopology();
// 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(20.0); // 20ps
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;
}
}
|
