Fast Motion

The first requirement is the definition of a low-dimensional space of reaction coordinates that still captures the essential dynamics of the processes we consider. Motions in the perpendicular null space should have irrelevant detail and equilibrate fast, preferably on a time scale that is separated from the time scale of the essential motions. Motions in the two spaces are separated much like is done in the Born-Oppenheimer approximation. The average influence of the fast motions on the essential degrees of freedom must be taken into account this concerns (i) correlations with positions expressed in a potential of mean force, (ii) correlations with velocities expressed in frictional terms, and iit) an uncorrelated remainder that can be modeled by stochastic terms. Of course, this scheme is the general idea behind the well-known Langevin and Brownian dynamics. [Pg.20]

An interesting approach has recently been chosen in the MBO(N)D program ([Moldyn 1997]). Structural elements of different size varying from individual peptide planes up to protein domains can be defined to be rigid. During an atomistic molecular dynamics simulation, all fast motion orthogonal to the lowest normal modes is removed. This allows use of ca. 20 times longer time steps than in standard simulations. [Pg.73]

The skeletal LN procedure is a dual timestep scheme, At, Atm, of two practical tasks (a) constructing the Hessian H in system (17) every Atm interval, and (b) solving system (17), where R is given by eq. (3), at the timestep At by procedure (23) outlined for LIN above. When a force-splitting procedure is also applied to LN, a value At > Atm is used to update the slow forces less often than the linearized model. A suitable frequency for the linearization is 1-3 fs (the smaller value is used for water systems), and the appropriate inner timestep is 0.5 fs, as in LIN. This inner timestep parallels the update frequency of the fast motions in force splitting approaches, and the linearization frequency Atm) is analogous to the medium timestep used in such three-class schemes (see below). [Pg.251]

As discussed above the errors in the trajectory are correlated with the missing rapid motions. In contrast to the friction approach of estimating the variance, which may affect long time phenomena, we identify our errors as the missing ( filtered ) high frequency modes. We therefore attempt to account approximately for the fast motions by choosing the trajectory variance accordingly. [Pg.274]

For the slow (y) motion the time step At may be chosen large whereas for the fast motion this time will be too large. Thus this propagator can be expressed as ... [Pg.304]

QCMD describes a coupling of the fast motions of a quantum particle to the slow motions of a classical particle. In order to classify the types of coupled motion we eventually have to deal with, we first analyze the case of an extremely heavy classical particle, i.e., the limit M —> oo or, better, m/M 0. In this adiabatic limit , the classical motion is so slow in comparison with the quantal motion that it cannot induce an excitation of the quantum system. That means, that the populations 6k t) = of the... [Pg.398]

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. [Pg.93]

The widths of the broad Lorentzians representing fast motions in the plane and perpendicular to the plane of the bilayer are compared in Ligures 12a and 12b, respectively. Only data at the lower hydration (23%) are available for comparison, and these agree well with the MD results, which show a slow, monotonic increase with Q. Although we expect the fast process to be at most only weakly dependent on hydration, it is not clear to what extent the comparison validates the simulation. [Pg.481]

It should be noted that there is a considerable difference between rotational structure narrowing caused by pressure and that caused by motional averaging of an adiabatically broadened spectrum [158, 159]. In the limiting case of fast motion, both of them are described by perturbation theory, thus, both widths in Eq. (3.16) and Eq (3.17) are expressed as a product of the frequency dispersion and the correlation time. However, the dispersion of the rotational structure (3.7) defined by intramolecular interaction is independent of the medium density, while the dispersion of the vibrational frequency shift (5 12) in (3.21) is linear in gas density. In principle, correlation times of the frequency modulation are also different. In the first case, it is the free rotation time te that is reduced as the medium density increases, and in the second case, it is the time of collision tc p/ v) that remains unchanged. As the density increases, the rotational contribution to the width decreases due to the reduction of t , while the vibrational contribution increases due to the dispersion growth. In nitrogen, they are of comparable magnitude after the initial (static) spectrum has become ten times narrower. At 77 K the rotational relaxation contribution is no less than 20% of the observed Q-branch width. If the rest of the contribution is entirely determined by... [Pg.115]

It is considered that the transition from d to d completely removes the fast motion with eigenfrequencies of H0 peculiar to the former, leaving behind only slow decay with relaxation time equal to or greater than V Since the other cofactor in the integrand of Eq. (4.26), M(t), decays much more rapidly (with time tc [Pg.139]

Short replication cycles that may be completed within a few hours, a large amount of viral progeny from one infected host-cell, as well as the general inaccuracy of viral nucleic acid polymerases result in an evolution occurring in fast motion, allowing rapid adaptation of viruses to selective pressures (see chapter by Boucher and Nijhius, this volume). Generalizing, it can be stated that any effective antiviral therapy will lead to the occurrence of resistance mutations. A well studied example... [Pg.18]

We also emphasize that the MD model does include the vibrational motions of bond, and torsional angles (in the minima of the respective potentials) but, somehow, these small scale fast motions are rapidly damped out in the melt, and do not affect the motion on the nanometer scale (and for corresponding times) significantly. [Pg.116]

The relationship between Ti and T2 was examined for a number of liquid alkanes and crude oils [15]. It was concluded that there is no difference for light oils, apparently because light oils satisfy the fast-motion condition (the correlation time is less than the Larmor period). However, viscous oils do not satisfy this condition as the departure between Tx and T2 correlates with an increasing viscosity and Larmor frequency. [Pg.325]

There is a second relaxation process, called spin-spin (or transverse) relaxation, at a rate controlled by the spin-spin relaxation time T2. It governs the evolution of the xy magnetisation toward its equilibrium value, which is zero. In the fluid state with fast motion and extreme narrowing 7) and T2 are equal in the solid state with slow motion and full line broadening T2 becomes much shorter than 7). The so-called 180° pulse which inverts the spin population present immediately prior to the pulse is important for the accurate determination of T and the true T2 value. The spin-spin relaxation time calculated from the experimental line widths is called T2 the ideal NMR line shape is Lorentzian and its FWHH is controlled by T2. Unlike chemical shifts and spin-spin coupling constants, relaxation times are not directly related to molecular structure, but depend on molecular mobility. [Pg.327]

Fast motions of the molecules in the liquid state average all these interactions. Chemical shifts and J values are measured as discrete averages, and the dipolar and quadrupolar interactions are averaged to zero. [Pg.73]

In impure metals, dislocation motion ocures in a stick-slip mode. Between impurities (or other point defects) slip occurs, that is, fast motion limited only by viscous drag. At impurities, which are usually bound internally and to the surrounding matrix by covalent bonds, dislocations get stuck. At low temperatures, they can only become freed by a quantum mechanical tunneling process driven by stress. Thus this part of the process is mechanically, not thermally, driven. The description of the tunneling rate has the form of Equation (4.3). Overall, the motion has two parts the viscous part and the tunneling part. [Pg.62]

LIG. 22 A schematic illustration of the dependence of NMR relaxation times T and T2 on the molecular correlation time, xc, characterizing molecular mobility in a singlecomponent system. Both slow and fast motions are effective for T2 relaxation, but only fast motions near w0 are effective in Tx relaxation. [Pg.47]

At temperatures around 50-60°C the three-site jump model is not a good approximation to the multi-site jump model, because the motion is not sufficiently rapid to be in the fast motion limit. However, the calculated spectra are fairly fitted with the observed ones. This is because the calculated spectrum is a superposition of constituent spectra whose rates are spread over several orders, so that the resultant spectrum is governed by the constituent spectra in the fast and slow motion limits having greater intensity than that in the intermediate exchange regime. [Pg.319]

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