constant-temperature molecular dynamics simulations
نویسندگان
چکیده
We discuss the use of a Langevin equation with a colored (correlated) noise to perform constanttemperature molecular dynamics simulations. Since the equations of motion are linear in nature, it is easy to predict the response of a Hamiltonian system to such a thermostat and to tune at will the relaxation time of modes of different frequency. This allows one to optimize the time needed to thermalize the system and generate independent configurations. We show how this frequency-dependent response can be exploited to control the temperature of Car-Parrinello-like dynamics, keeping at low temperature the electronic degrees of freedom, without affecting the adiabatic separation from the vibrations of the ions.
منابع مشابه
Molecular Dynamics Simulation of Potassium Chloride Melting (II. Constant Volume and Constant Pressure Simulation of Filled System)
We have used a simple ionic potential to simulate the melting of KCI pseudo-infinite crystal. Two MD simulations, one with constant Volume and the other with constant pressure condition are performed. These results are compared with the previous micro-sample simulation results. In the constant volume simulation the melting temperature increase substantially with increasing pressure. A method fo...
متن کاملMechanical Characteristics and Failure Mechanism of Nano-Single Crystal Aluminum Based on Molecular Dynamics Simulations: Strain Rate and Temperature Effects
Besides experimental methods, numerical simulations bring benefits and great opportunities to characterize and predict mechanical behaviors of materials especially at nanoscale. In this study, a nano-single crystal aluminum (Al) as a typical face centered cubic (FCC) metal was modeled based on molecular dynamics (MD) method and by applying tensile and compressive strain loadings its mechanical ...
متن کاملGyration Radius and Energy Study at Different Temperatures for Acetylcholine Receptor Protein in Gas Phase by Monte Carlo, Molecular and Langevin Dynamics Simulations
The determination of gyration radius is a strong research for configuration of a Macromolecule. Italso reflects molecular compactness shape. In this work, to characterize the behavior of theprotein, we observe quantities such as the radius of gyration and the average energy. We studiedthe changes of these factors as a function of temperature for Acetylcholine receptor protein in gasphase with n...
متن کاملElastic Properties and Fracture Analysis of Perfect and Boron-doped C2N-h2D Using Molecular Dynamics Simulation
This paper explores the mechanical properties and fracture analysis of C2N-h2D single-layer sheets using classical molecular dynamics (MD) simulations. Simulations are carried out based on the Tersoff potential energy function within Nose-Hoover thermostat algorithm at the constant room temperature in a canonical ensemble. The influences of boron (B) doping on the mechanical properties, ...
متن کاملEnergy study at different solvents for potassium Channel Protein by Monte Carlo, Molecular and Langevin Dynamics Simulations
Potassium Channels allow potassium flux and are essential for the generation of electric current acrossexcitable membranes. Potassium Channels are also the targets of various intracellular controlmechanisms; such that the suboptimal regulation of channel function might be related to pathologicalconditions. Realistic studies of ion current in biologic channels present a major challenge for compu...
متن کاملTemperature Effect on Mechanical Properties of Top Neck Mollusk Shells Nano-Composite by Molecular Dynamics Simulations and Nano-Indentation Experiments
Discovering the mechanical properties of biological composite structures at the Nano-scale is much interesting today. Top Neck mollusk shells are amongst biomaterials Nano-Composite that their layered structures are composed of organic and inorganic materials. Since the Nano indentation process is known as an efficient method to determine mechanical properties like elastic modulus and hardness ...
متن کامل