home
about
news
download
doc
source
systems
tests
bugs
contact
IMP Reference Guide
2.6.1
The Integrative Modeling Platform
IMP Manual
Reference Guide
Modules
Classes
Examples
include
IMP
atom
BrownianDynamicsTAMD.h
Go to the documentation of this file.
1
/**
2
* \file IMP/atom/BrownianDynamicsTAMD.h
3
* \brief Simple molecular dynamics optimizer.
4
*
5
* Copyright 2007-2016 IMP Inventors. All rights reserved.
6
*
7
*/
8
9
#ifndef IMPATOM_BROWNIAN_DYNAMICS_TAMD_H
10
#define IMPATOM_BROWNIAN_DYNAMICS_TAMD_H
11
12
#include <IMP/atom/atom_config.h>
13
#include "
Diffusion.h
"
14
#include "
atom_macros.h
"
15
#include <
IMP/atom/BrownianDynamics.h
>
16
#include <
IMP/Particle.h
>
17
#include <
IMP/Optimizer.h
>
18
#include <IMP/internal/units.h>
19
#include <
IMP/algebra/Vector3D.h
>
20
21
IMPATOM_BEGIN_NAMESPACE
22
23
// for swig
24
class
SimulationParameters;
25
26
//! Simple Brownian dynamics simulator.
27
/** This is an implementation of a Brownian Dynamics simulator.
28
29
_Input particles and score_
30
31
Each optimized particle must have x,y,z attributes
32
that are optimizable. In addition, each optimized particle must be
33
decorated with the Diffusion decorator. Optionally, the
34
RigidBodyDiffusion decorator can be used to specify a rotational
35
diffusion coefficient for core::RigidBody particles. The
36
optimizer assumes the scoring function to be energy in kcal/mol, and the xyz
37
coordinates to be in angstroms and the diffusion coefficient of
38
each particle be in \f$A^2/fs\f$ (or \f$Radian^2/fs\f$ for rotational
39
diffusion coefficient). Particles without optimized x,y,z
40
and nonoptimized D are skipped.
41
42
The optimizer can either automatically determine which particles
43
to use from the model or be passed a SingletonContainer for the
44
particles. If such a container is passed, particles added to it
45
during optimization state updates are handled properly.
46
47
_Simulation_
48
49
At each simulation time step, each particle is translated in the
50
direction of the sum of a random diffusion vector and the gradient
51
of the scoring function (force field) at the particle
52
coordinates. The translation is proportional to the particle
53
diffusion coefficient, the time step size, and the inverse of kT.
54
Note that particles masses are not considered, only their
55
diffusion coefficients.
56
57
Similarly, rigid bodies are rotated by the sum of a random torque and a
58
force field torque, proportionally to the rotational diffusion
59
coefficient, the time step size, and inversely proportional kT.
60
61
If the skt (stochastic runge kutta) flag is true, the simulation is
62
altered slightly to apply the SKT scheme.
63
64
\see Diffusion
65
\see RigidBodyDiffusion
66
*/
67
class
IMPATOMEXPORT
BrownianDynamicsTAMD
:
public
BrownianDynamics
{
68
public
:
69
//! Create the optimizer
70
/** If sc is not null, that container will be used to find particles
71
to move, otherwise the model will be searched.
72
@param m model associated with bd
73
@param name name of bd object
74
@param wave_factor for wave step function, see Simulator object,
75
if >1.001 or so, creates a wave of time steps
76
that are larger by up to wave_factor from
77
formal maximal time step
78
79
@note wave_factor is an advanced feature - if you're not sure, just use
80
its default, see also Simulator::simulate_wave()
81
*/
82
BrownianDynamicsTAMD
(
Model
*m,
83
std::string name =
"BrownianDynamicsTAMD%1%"
,
84
double
wave_factor = 1.0);
85
86
protected
:
87
/** advances a chunk of ps from index begin to end
88
89
@param dtfs time step in femtoseconds
90
@param ikt inverse kT for current chunk step
91
@param ps particle indexes to advance
92
@param begin beginning index of chunk of ps
93
@param end end index of chunk of ps
94
*/
95
void
do_advance_chunk
(
double
dtfs,
double
ikt,
96
const
ParticleIndexes
&ps,
97
unsigned
int
begin,
unsigned
int
end)
98
IMP_OVERRIDE
;
99
100
private
:
101
void
advance_coordinates_1(
ParticleIndex
pi,
unsigned
int
i,
102
double
dtfs,
double
ikT);
103
void
advance_coordinates_0(
ParticleIndex
pi,
unsigned
int
i,
104
double
dtfs,
double
ikT);
105
void
advance_orientation_0(
ParticleIndex
pi,
double
dtfs,
double
ikT);
106
};
107
108
IMPATOM_END_NAMESPACE
109
110
#endif
/* IMPATOM_BROWNIAN_DYNAMICS_TAMD_H */
Diffusion.h
A decorator for a diffusing particle.
BrownianDynamics.h
Simple molecular dynamics optimizer.
IMP::Index< ParticleIndexTag >
IMP::atom::BrownianDynamicsTAMD
Simple Brownian dynamics simulator.
Definition:
BrownianDynamicsTAMD.h:67
Optimizer.h
Base class for all optimizers.
IMP::Vector< ParticleIndex >
IMP::Model
Class for storing model, its restraints, constraints, and particles.
Definition:
Model.h:72
IMP::atom::BrownianDynamics
Simple Brownian dynamics simulator.
Definition:
BrownianDynamics.h:74
IMP::atom::BrownianDynamics::do_advance_chunk
virtual void do_advance_chunk(double dtfs, double ikt, const ParticleIndexes &ps, unsigned int begin, unsigned int end)
Particle.h
Classes to handle individual model particles. (Note that implementation of inline functions is in int...
atom_macros.h
Various important macros for implementing decorators.
Vector3D.h
Simple 3D vector class.
IMP_OVERRIDE
#define IMP_OVERRIDE
Cause a compile error if this method does not override a parent method.
Definition:
compiler_macros.h:80