Maintains temperature during molecular dynamics. More...
#include <IMP/atom/BerendsenThermostatOptimizerState.h>
Inheritance diagram for IMP::atom::BerendsenThermostatOptimizerState:Public Member Functions | |
| BerendsenThermostatOptimizerState (const Particles &pis, double temperature, double tau) | |
| virtual void | do_show (std::ostream &out) const |
| double | get_tau () |
| double | get_temperature () |
| void | rescale_velocities () const |
| Rescale the velocities now. | |
| void | set_particles (const Particles &pis) |
| Set the particles to use. | |
| void | set_tau (double tau) |
| void | set_temperature (double temperature) |
| virtual void | update () |
| Called when the Optimizer accepts a new conformation. | |
| Public Member Functions inherited from IMP::kernel::OptimizerState | |
| OptimizerState (std::string name="OptimizerState %1%") | |
| Optimizer * | get_optimizer () const |
| virtual void | set_is_optimizing (bool) |
| Public Member Functions inherited from IMP::base::Object | |
| virtual void | clear_caches () |
| virtual IMP::base::VersionInfo | get_version_info () const =0 |
| Get information about the module and version of the object. | |
| void | set_check_level (CheckLevel l) |
| void | set_log_level (LogLevel l) |
| Set the logging level used in this object. More... | |
| void | set_was_used (bool tf) const |
| void | show (std::ostream &out=std::cout) const |
| const std::string & | get_name () const |
| void | set_name (std::string name) |
Related Functions | |
(Note that these are not member functions.) | |
| typedef IMP::base::Vector < IMP::base::WeakPointer < BerendsenThermostatOptimizerState > > | BerendsenThermostatOptimizerStatesTemp |
| Related Functions inherited from IMP::kernel::OptimizerState | |
| typedef IMP::base::Vector < IMP::base::WeakPointer < OptimizerState > > | OptimizerStatesTemp |
| Related Functions inherited from IMP::base::Object | |
| typedef IMP::base::Vector < IMP::base::WeakPointer < Object > > | ObjectsTemp |
Additional Inherited Members | |
| Protected Member Functions inherited from IMP::base::Object | |
| Object (std::string name) | |
| Construct an object with the given name. More... | |
| Protected Attributes inherited from IMP::kernel::OptimizerState | |
| UncheckedWeakPointer< Optimizer > | optimizer_ |
Detailed Description
The thermostat scales velocities using the algorithm described in H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. DiNola, and J. R. Haak "Molecular dynamics with coupling to an external bath", Journal of Chemical Physics 81 pp. 3684-3690 (1984).
At each update, velocities are rescaled by
\[ \lambda = \left[1 + \frac{\Delta t}{\tau_T} \left( \frac{T}{T_k} -1\right)\right]^{1/2} \]
where \(\Delta t\) is the molecular dynamics timestep, \(\tau_T\) is the coupling constant (in fs) of the thermostat, \(T\) is the thermostat temperature, and \(T_k\) is the instantaneous (kinetic) temperature of the dynamics. (This is equation 11 from the reference above.)
Definition at line 37 of file BerendsenThermostatOptimizerState.h.
Friends And Related Function Documentation
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related |
Pass a set of objects.
Definition at line 81 of file BerendsenThermostatOptimizerState.h.
The documentation for this class was generated from the following file: