Molecular dynamics regularity

Snapshots at regular time intervals that store atomic coordi-riaies and velocities. You can play back these snapshots to inspect the simulated structures or to average values. Yon specify a Snapshot period in the Molecular Dynamics Snapshots dialog box. 

TlyperCi hem updates the screen diirin g a trajectory at regular in ter-vals so yon can visiiali/e the irajectory. Since this screen update may slow down a trajectory If it occurs too frequently, yon c.an specify the duration of the Screen Refresh period At.,. The screen updates at ilines tQ, Iq + Atj, to + 2Atj, etc. The Screen Refresh period is specified in the Molecular Dynamics options dialog box by n 5 data steps, i.e. as a m iiliiplc of the data collection period, At5 = n 5 At2-... 

Averages or plotted values at regular time intervals. You specify an Average/Graph period in the Molecular Dynamics Averages dialog box. 

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. 

In a normal molecular dynamics simulation with repeating boundary conditions (i.e., periodic boundary condition), the volume is held fixed, whereas at constant pressure the volume of the system must fluemate. In some simulation cases, such as simulations dealing with membranes, it is more advantageous to use the constant-pressure MD than the regular MD. Various schemes for prescribing the pressure of a molecular dynamics simulation have also been proposed and applied [23,24,28,29]. In all of these approaches it is inevitable that the system box must change its volume. 

These difficulties can be circumvented by using the adaptive biasing force (ABF) method of Darve, Pohorille, and coworkers [18, 28, 29], which is based on unconstrained molecular dynamics simulations. This is a very efficient approach which begins by establishing a simple formula to calculate d,4/d from regular molecular dynamics in which is not constrained. This derivative represents the mean force acting on . Therefore if we remove this force from the system we obtain... 

An overreaching theme of the present chapter, besides broken ergodicity, has to do with the fact that most of the enhanced sampling methods that we shall discuss address situations in which one cannot clearly identify a reaction coordinate that can be conveniently used to describe the kinetic evolution of the system of interest. While methods for enhanced sampling are designed to yield accurate results faster than regular molecular dynamics or Monte Carlo (MC) methods, it is our belief that there is no perfect method, but that, rather, there are methods that perform better for particular applications. Moreover, it should be noted that, while in instances when a proper reaction coordinate can be identified methods described in other chapters are probably more efficient, they could still benefit by sampling in conformational directions perpendicular to the reaction coordinate. 

A conformational analysis, by NMR and molecular dynamics,116 of a cyclic C-glycosyl analogue of p-GlcNAc-Asn demonstrated some variations in relation to the conformation of the regular A-glycosyl analogue. 

General regularities of molecular dynamics and local organization of micellar phase of polyelectrolytes complexes with ionic SAS [16-22, 26] were formulated for the solution of this problem spin probes were used. Formulas of some of the last ones are presented in Scheme 3. 

Let consider regularities of molecular dynamics of micellar phase of complexes polyacid-SAS on the example of PMAA complexes with dodecylsubstituted polyethylene glycol (DD-PEG, formula is presented below) [22, 23], Analogous regularities were observed under investigation of PAA complexes with DD-PEG [24],... 

Obtained results allow formulating general regularities of molecular dynamics of detergent molecules in micellar phase of polyacids complexes with nonionic SAS. 

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