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IMP Reference Guide
2.11.0
The Integrative Modeling Platform
IMP Manual
Reference Guide
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include
IMP
atom
version 2.11.0
BrownianDynamicsTAMD.h
Go to the documentation of this file.
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/**
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* \file IMP/atom/BrownianDynamicsTAMD.h
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* \brief Simple molecular dynamics optimizer.
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*
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* Copyright 2007-2019 IMP Inventors. All rights reserved.
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*
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*/
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#ifndef IMPATOM_BROWNIAN_DYNAMICS_TAMD_H
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#define IMPATOM_BROWNIAN_DYNAMICS_TAMD_H
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#include <IMP/atom/atom_config.h>
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#include "
Diffusion.h
"
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#include "
atom_macros.h
"
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#include <
IMP/algebra/Sphere3D.h
>
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#include <
IMP/atom/BrownianDynamics.h
>
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#include <
IMP/Particle.h
>
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#include <
IMP/Optimizer.h
>
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#include <IMP/internal/units.h>
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#include <
IMP/algebra/Vector3D.h
>
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IMPATOM_BEGIN_NAMESPACE
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// for swig
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class
SimulationParameters;
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//! Simple Brownian dynamics simulator.
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/** This is an implementation of a Brownian Dynamics simulator.
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_Input particles and score_
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Each optimized particle must have x,y,z attributes
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that are optimizable. In addition, each optimized particle must be
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decorated with the Diffusion decorator. Optionally, the
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RigidBodyDiffusion decorator can be used to specify a rotational
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diffusion coefficient for core::RigidBody particles. The
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optimizer assumes the scoring function to be energy in kcal/mol, and the xyz
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coordinates to be in angstroms and the diffusion coefficient of
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each particle be in \f$A^2/fs\f$ (or \f$Radian^2/fs\f$ for rotational
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diffusion coefficient). Particles without optimized x,y,z
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and nonoptimized D are skipped.
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The optimizer can either automatically determine which particles
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to use from the model or be passed a SingletonContainer for the
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particles. If such a container is passed, particles added to it
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during optimization state updates are handled properly.
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_Simulation_
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At each simulation time step, each particle is translated in the
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direction of the sum of a random diffusion vector and the gradient
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of the scoring function (force field) at the particle
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coordinates. The translation is proportional to the particle
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diffusion coefficient, the time step size, and the inverse of kT.
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Note that particles masses are not considered, only their
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diffusion coefficients.
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Similarly, rigid bodies are rotated by the sum of a random torque and a
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force field torque, proportionally to the rotational diffusion
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coefficient, the time step size, and inversely proportional kT.
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If the skt (stochastic runge kutta) flag is true, the simulation is
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altered slightly to apply the SKT scheme.
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_Time step_
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The time step is always equal precisely to Simulater::get_maximum_time_step()
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when using either Simulator::simulate() or Optimizer::optimize()
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\see Diffusion
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\see RigidBodyDiffusion
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*/
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class
IMPATOMEXPORT
BrownianDynamicsTAMD
:
public
BrownianDynamics
{
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public
:
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//! Create the optimizer
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/** If sc is not null, that container will be used to find particles
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to move, otherwise the model will be searched.
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@param m model associated with bd
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@param name name of bd object
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@param wave_factor for wave step function, see Simulator object,
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if >1.001 or so, creates a wave of time steps
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that are larger by up to wave_factor from
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formal maximal time step
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@note wave_factor is an advanced feature - if you're not sure, just use
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its default, see also Simulator::simulate_wave()
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*/
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BrownianDynamicsTAMD
(
Model
*m,
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std::string name =
"BrownianDynamicsTAMD%1%"
,
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double
wave_factor = 1.0);
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protected
:
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/** advances a chunk of ps from index begin to end
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@param dtfs time step in femtoseconds
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@param ikt inverse kT for current chunk step
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@param ps particle indexes to advance
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@param begin beginning index of chunk of ps
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@param end end index of chunk of ps
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*/
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void
do_advance_chunk
(
double
dtfs,
double
ikt,
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const
ParticleIndexes
&ps,
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unsigned
int
begin,
unsigned
int
end)
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IMP_OVERRIDE
;
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private
:
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void
advance_coordinates_1(
ParticleIndex
pi,
unsigned
int
i,
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double
dtfs,
double
ikT,
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double
diffusion_coefficient,
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algebra::Sphere3D
const
& xyzr_derivative_pi);
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void
advance_coordinates_0(
unsigned
int
i,
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double
dtfs,
double
ikT,
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double
diffusion_coefficient,
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algebra::Sphere3D
const
& xyzr_derivative_pi,
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algebra::Sphere3D
& xyzr_access);
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inline
algebra::Rotation3D
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compute_rotation_0(
ParticleIndex
pi,
double
dtfs,
double
ikT,
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double
rotational_diffusion_coefficient_table,
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double
const
* torque_tables[]) ;
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};
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IMPATOM_END_NAMESPACE
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#endif
/* IMPATOM_BROWNIAN_DYNAMICS_TAMD_H */
Diffusion.h
A decorator for a diffusing particle.
BrownianDynamics.h
Simple Brownian dynamics optimizer.
IMP::Index< ParticleIndexTag >
IMP::atom::BrownianDynamicsTAMD
Simple Brownian dynamics simulator.
Definition:
BrownianDynamicsTAMD.h:72
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:80
IMP::atom::BrownianDynamics::do_advance_chunk
virtual void do_advance_chunk(double dtfs, double ikt, const ParticleIndexes &ps, unsigned int begin, unsigned int end)
IMP::algebra::Rotation3D
3D rotation class.
Definition:
Rotation3D.h:46
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.
Sphere3D.h
Simple 3D sphere class.
IMP::algebra::SphereD< 3 >
IMP_OVERRIDE
#define IMP_OVERRIDE
Cause a compile error if this method does not override a parent method.
Definition:
compiler_macros.h:78