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
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
|
/* -------------------------------------------------------------------------- *
* SimTK Core: SimTK Simbody(tm) *
* -------------------------------------------------------------------------- *
* 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 <fstream>
using namespace SimTK;
using namespace std;
namespace SimTK {
}
int main() {
try
{
CompoundSystem system; // molecule-specialized simbody System
SimbodyMatterSubsystem matter(system);
DuMMForceFieldSubsystem dumm(system); // molecular force field
// MagnesiumIon mg1, mg2;
MagnesiumIon::setAmberLikeParameters(dumm);
MagnesiumIon mg1;
system.adoptCompound(mg1, Vec3(-0.5, 1, 0));
system.modelCompounds();
const State& state = system.realizeTopology();
system.realize(state, Stage::Dynamics);
Vec3 mg1Force = system.getRigidBodyForces(state, Stage::Dynamics)
[mg1.getAtomMobilizedBodyIndex(Compound::AtomIndex(0))][1];
cout << "Force on first magnesium = " << mg1Force << endl;
cout << "Mobilized body Id " << mg1.getAtomMobilizedBodyIndex(Compound::AtomIndex(0)) << endl;
Real JouleToCalorie = 1.0 / 4.184;
Real potentialEnergy = system.calcPotentialEnergy(state) * JouleToCalorie;
cout << "Energy = " << potentialEnergy << " kcal/mole" << endl;
// Experimental value is -455.5 kcal/mole, from Rosseinsky (1965) Chem. Rev. 65: 467-490
// accuracy is greatly affected by estimate of H+ solvation free energy
Real expectedEnergy = -455.5;
Real deltaV = potentialEnergy - expectedEnergy;
// ensure potential is within 20 kcals of experimental value, or 400 kcal^2 of squared value
SimTK_ASSERT_ALWAYS(deltaV*deltaV < 400, (String("Expected Mg+2 solvation energy of ") + String(expectedEnergy) + ", found energy of " + String(potentialEnergy)).c_str() );
}
catch (const std::exception& e)
{
printf("EXCEPTION THROWN: %s\n", e.what());
}
catch (...)
{
printf("UNKNOWN EXCEPTION THROWN\n");
} return 0;
}
|
