Langevin equation motion

In an early study of lysozyme ([McCammon et al. 1976]), the two domains of this protein were assumed to be rigid, and the hinge-bending motion in the presence of solvent was described by the Langevin equation for a damped harmonic oscillator. The angular displacement 0 from the equilibrium position is thus governed by... 

The LIN method ( Langevin/Implicit/Normal-Modes ) combines frequent solutions of the linearized equations of motions with anharmonic corrections implemented by implicit integration at a large timestep. Namely, we express the collective position vector of the system as X t) = Xh t) + Z t). (In LN, Z t) is zero). The first part of LIN solves the linearized Langevin equation for the harmonic reference component of the motion, Xh t)- The second part computes the residual component, Z(t), with a large timestep. 

We further discuss how quantities typically measured in the experiment (such as a rate constant) can be computed with the new formalism. The computations are based on stochastic path integral formulation [6]. Two different sources for stochasticity are considered. The first (A) is randomness that is part of the mathematical modeling and is built into the differential equations of motion (e.g. the Langevin equation, or Brownian dynamics). The second (B) is the uncertainty in the approximate numerical solution of the exact equations of motion. 

For example, the SHAKE algorithm [17] freezes out particular motions, such as bond stretching, using holonomic constraints. One of the differences between SHAKE and the present approach is that in SHAKE we have to know in advance the identity of the fast modes. No such restriction is imposed in the present investigation. Another related algorithm is the Backward Euler approach [18], in which a Langevin equation is solved and the slow modes are constantly cooled down. However, the Backward Euler scheme employs an initial value solver of the differential equation and therefore the increase in step size is limited. 

Langevin dynamics simulates the effect of molecular collisions and the resulting dissipation of energy that occur in real solvents, without explicitly including solvent molecules. This is accomplished by adding a random force (to model the effect of collisions) and a frictional force (to model dissipative losses) to each atom at each time step. Mathematically, this is expressed by the Langevin equation of motion (compare to Equation (22) in the previous chapter) ... 

When the friction coefficient is set to zero, HyperChem performs regular molecular dynamics, and one should use a time step that is appropriate for a molecular dynamics run. With larger values of the friction coefficient, larger time steps can be used. This is because the solution to the Langevin equation in effect separates the motions of the atoms into two time scales the short-time (fast) motions, like bond stretches, which are approximated, and longtime (slow) motions, such as torsional motions, which are accurately evaluated. As one increases the friction coefficient, the short-time motions become more approximate, and thus it is less important to have a small timestep. 

The friction coefficient determines the strength of the viscous drag felt by atoms as they move through the medium its magnitude is related to the diffusion coefficient, D, through the relation Y= kgT/mD. Because the value of y is related to the rate of decay of velocity correlations in the medium, its numerical value determines the relative importance of the systematic dynamic and stochastic elements of the Langevin equation. At low values of the friction coefficient, the dynamical aspects dominate and Newtonian mechanics is recovered as y —> 0. At high values of y, the random collisions dominate and the motion is diffusion-like. 

The basic equation of motion for stochastic dynamics is the Langevin equation. 

An algorithm for performing a constant-pressure molecular dynamics simulation that resolves some unphysical observations in the extended system (Andersen s) method and Berendsen s methods was developed by Feller et al. [29]. This approach replaces the deterministic equations of motion with the piston degree of freedom added to the Langevin equations of motion. This eliminates the unphysical fluctuation of the volume associated with the piston mass. In addition, Klein and coworkers [30] present an advanced constant-pressure method to overcome an unphysical dependence of the choice of lattice in generated trajectories. 

The classical motion of a particle interacting with its environment can be phenomenologically described by the Langevin equation... 

Second, the classical dynamics of this model is governed by the generalized Langevin equation of motion in the adiabatic barrier [Zwanzig 1973 Hanggi et al. 1990 Schmid 1983],... 

Altenberger and Tirrell [11] utilized the Langevin equation for particle motion coupled with hydrodynamics described by the Navier-S takes equation to determine particle diffusion coefficients in porous media given by... 

The friction coefficient is one of the essential elements in the Langevin description of Brownian motion. The derivation of the Langevin equation from the microscopic equations of motion provides a Green-Kubo expression for this transport coefficient. Its computation entails a number of subtle features. Consider a Brownian (B) particle with mass M in a bath of N solvent molecules with mass m. The generalized Langevin equation for the momentum P of the B... 

Brownian motion theory may be generalized to treat systems with many interacting B particles. Such many-particle Langevin equations have been investigated at a molecular level by Deutch and Oppenheim [58], A simple system in which to study hydrodynamic interactions is two particles fixed in solution at a distance Rn- The Langevin equations for the momenta P, (i = 1,2)... 

The concept of the TS trajectory was first introduced [37] in the context of stochastically driven dynamics described by the Langevin equation of motion... 

Following the general procedure of geometric TST, we start by discussing the linearized dynamics in relative coordinates. If the definition (41) is substituted into the linearized Langevin equation (13), it yields an equation of motion for the relative coordinate ... 

The earliest and simplest approach in this direction starts from Langevin equations with solutions comprising a spectrum of relaxation modes [1-4], Special features are the incorporation of entropic forces (Rouse model, [6]) which relax fluctuations of reduced entropy, and of hydrodynamic interactions (Zimm model, [7]) which couple segmental motions via long-range backflow fields in polymer solutions, and the inclusion of topological constraints or entanglements (reptation or tube model, [8-10]) which are mutually imposed within a dense ensemble of chains. 

In order to proceed now to a statistical mechanical description of the corresponding relaxation process, it is convenient to solve the equation of motion for the creation and destruction operators and cast them in a form ressembling a Generalized Langevin equation. We will only sketch the procedure. 

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