Rescaling

As data of the binary diflfiision coefficient Dam(P> tne not available in many cases, one has to resort to taking the solvent self-diflfiision coefficient Dy p,T) which requires rescaling in the low-pressure regime according to... 

Experimentally, tire hard-sphere phase transition was observed using non-aqueous polymer lattices [79, 80]. Samples are prepared, brought into the fluid state by tumbling and tlien left to stand. Depending on particle size and concentration, colloidal crystals tlien fonn on a time scale from minutes to days. Experimentally, tliere is always some uncertainty in the actual volume fraction. Often tire concentrations are tlierefore rescaled so freezing occurs at ( )p = 0.49. The widtli of tire coexistence region agrees well witli simulations [Jd, 80]. 

We will focus on one experimental study here. Monovoukas and Cast studied polystyrene particles witli a = 61 nm in potassium chloride solutions [86]. They obtained a very good agreement between tlieir observations and tire predicted Yukawa phase diagram (see figure C2.6.9). In order to make tire comparison tliey rescaled the particle charges according to Alexander et al [43] (see also [82]). At high electrolyte concentrations, tire particle interactions tend to hard-sphere behaviour (see section C2.6.4) and tire phase transition shifts to volume fractions around 0.5 [88]. 

In the q = l limit, the effective temperature equals the standard temperature. Otherwise, adding a constant shift to the potential energy is equivalent to rescaling the temperature at which the canonical probability distribution is computed. 

The algorithm of Hao et al. [30] essentially minimizes X), eq. (8), at each step to obtain and then adds to it a rescaled velocity term to... 

By assumption, the mass ratio = m/M is a small parameter. Thus, rescaling the Schrbdinger equation properly in time and potential transforms it into the singularly perturbed equation... 

However, it is common practice to sample an isothermal isobaric ensemble NPT, constant pressure and constant temperature), which normally reflects standard laboratory conditions well. Similarly to temperature control, the system is coupled to an external bath with the desired target pressure Pq. By rescaling the dimensions of the periodic box and the atomic coordinates by the factor // at each integration step At according to Eq. (46), the volume of the box and the forces of the solvent molecules acting on the box walls are adjusted. 

In the heating phase (assuming i j is non-zero), the velocities are periodically rescaled to change the system temperature from the initial tern perature T to the simulation temperature T2 in incrc-m eiiis of th e temperature step AT. Th e h eaiin g period for rescaling the velocities, P, is defined by ... 

The consistent force field (CFF) was developed to yield consistent accuracy of results for conformations, vibrational spectra, strain energy, and vibrational enthalpy of proteins. There are several variations on this, such as the Ure-Bradley version (UBCFF), a valence version (CVFF), and Lynghy CFF. The quantum mechanically parameterized force field (QMFF) was parameterized from ah initio results. CFF93 is a rescaling of QMFF to reproduce experimental results. These force fields use five to six valence terms, one of which is an electrostatic term, and four to six cross terms. 

If the heating time t or cooling time t are non-zero, or if the run time tj. is non-zero and constant temperature is selected, velocities are adjusted (rescaled) during the molecular dynamics run to change the temperature of the system. 

When using the heating and cooling features of HyperChem it should be remembered that it is accomplished through rescaling of the velocities, so if the velocities are zero no temperature can occur. This happens, for example, if you start with an exactly optimized structure and heat from a starting temperature Tj of zero, or use the restart option when velocities are all zero. 

Berendsen et al. [H. I. C. Berendsen, I. P. M. Postma, W. F. van Gun-steren, A. di Nola, and I. R. Haak, J. Chem. Phys. 81, 3684 (1984)] have described a simple scheme for constant temperature simulations that is implemented in HyperChem. You can use this constant temperature scheme by checking the constant temperature check box and specifying a bath relaxation constant t. This relaxation constant must be equal to or bigger than the dynamics step size D/. If it is equal to the step size, the temperature will be kept as close to constant as possible. This occurs, essentially, by rescaling the velocities used to update positions to correspond exactly to the specified initial temperature. For larger values of the relaxation constant, the temperature is kept approximately constant by superimposing a first-order relaxation process on the simulation. That is ... 

The first approach is based on introducing simple velocity or position rescaling into the standard Newtonian MD. The second approach has a dynamic origin and is based on a refonnulation of the Lagrangian equations of motion for the system (so-called extended Lagrangian formulation.) In this section, we discuss several of the most widely used constant-temperature or constant-pressure schemes. 

The simplest method that keeps the temperature of a system constant during an MD simulation is to rescale the velocities at each time step by a factor of (To/T) -, where T is the current instantaneous temperature [defined in Eq. (24)] and Tq is the desired temperamre. This method is commonly used in the equilibration phase of many MD simulations and has also been suggested as a means of performing constant temperature molecular dynamics [22]. A further refinement of the velocity-rescaling approach was proposed by Berendsen et al. [24], who used velocity rescaling to couple the system to a heat bath at a temperature Tq. Since heat coupling has a characteristic relaxation time, each velocity V is scaled by a factor X, defined as... 

An alternative procedure rescales the coordinates of each atom at each time step [24]. The atomic coordinate x and the characteristic distance for repeating boundary conditions, d, are rescaled to values uc and fid, respectively, where... 

In the structure with all the surfactant molecules located at monolayers, the volume fraction of surfactant should be proportional to the average surface area times the width of the monolayer divided by the volume, i.e., Ps (X Sa/V. The proportionality constant is called the surfactant parameter [34]. This is true for a single surface with no intersections. In our mesoscopic description the volume is measured in units of the volume occupied by the surfactant molecule, and the area is measured in units of the area occupied by the amphiphile. In other words, in our model the area of the monolayer is the dimensionless quantity equal to the number of amphiphiles residing on the monolayer. Hence, it should be identified with the area rescaled by the surfactant parameter of the corresponding structure. 

FIG. 3 Differential capacitance C as a function of a for several values of parameters. The parameters are given for 1 m aqueous solution and are rescaled... 

Here U = T — T )Cp/L is the appropriately rescaled temperature field T measured from the imposed temperature of the undercooled melt far away from the interface. The indices L and 5 refer to the liquid and solid, respectively, and the specific heat Cp and the thermal diffusion constant D are considered to be the same in both phases. L is the latent heat, and n is the normal to the interface. In terms of these parameters,... 

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