Explicit dynamic simulations

S. K. Gray, D. W. Noid and B. G. Sumpter, Symplectic integrators for large scale molecular dynamics simulations A comparison of several explicit methods , J. Chem. Phys., Vol 101, no 5, 4062-72, 1994. 

The explicit definition of water molecules seems to be the best way to represent the bulk properties of the solvent correctly. If only a thin layer of explicitly defined solvent molecules is used (due to hmited computational resources), difficulties may rise to reproduce the bulk behavior of water, especially near the border with the vacuum. Even with the definition of a full solvent environment the results depend on the model used for this purpose. In the relative simple case of TIP3P and SPC, which are widely and successfully used, the atoms of the water molecule have fixed charges and fixed relative orientation. Even without internal motions and the charge polarization ability, TIP3P reproduces the bulk properties of water quite well. For a further discussion of other available solvent models, readers are referred to Chapter VII, Section 1.3.2 of the Handbook. Unfortunately, the more sophisticated the water models are (to reproduce the physical properties and thermodynamics of this outstanding solvent correctly), the more impractical they are for being used within molecular dynamics simulations. 

The first molecular dynamics simulations of a lipid bilayer which used an explicit representation of all the molecules was performed by van der Ploeg and Berendsen in 1982 [van dei Ploeg and Berendsen 1982]. Their simulation contained 32 decanoate molecules arranged in two layers of sixteen molecules each. Periodic boundary conditions were employed and a xmited atom force potential was used to model the interactions. The head groups were restrained using a harmonic potential of the form ... 

Kim K S, M A Moller, D J Tildesley and N Quirke 1994a. Molecular Dynamics Simulations Langmuir-Blodgett Monolayers with Explicit Head-group Interactions. Molecular Simidati 13 77-99. 

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) ... 

Steady state analysis explicitly evaluates model parameters, Dynamic simulations predict reactor start-up transients. 

Tarek et al. [388] studied a system with some similarities to the work of Bocker et al. described earlier—a monolayer of n-tetradecyltrimethylammonium bromide. They also used explicit representations of the water molecules in a slab orientation, with the mono-layer on either side, in a molecular dynamics simulation. Their goal was to model more disordered, liquid states, so they chose two larger molecular areas, 0.45 and 0.67 nm molecule Density profiles normal to the interface were calculated and compared to neutron reflectivity data, with good agreement reported. The hydrocarbon chains were seen as highly disordered, and the diffusion was seen at both areas, with a factor of about 2.5 increase from the smaller molecular area to the larger area. They report no evidence of a tendency for the chains to aggregate into ordered islands, so perhaps this work can be seen as a realistic computer simulation depiction of a monolayer in an LE state. 

The theory was very similar to that described earlier, but was simplified in view of the complexity of the problem. A number of reaction intermediates were considered explicitly, and the corresponding signals were calculated by molecular dynamics simulation. Kinetic equations governing the reaction sequence were established and were solved numerically. The main simplification of the theory is that, when calculating A5[r, r], the lower limit of the Fourier integral was shifted from 0 to a small value q. The authors wrote [59]... 

Dimitrov, D. 1., Milchev, A. and Binder, K (2007) Polymer brushes in solvents of variable quality Molecular dynamics simulations using explicit solvent./. Chem. Phys., 127, 084905. 

Equilibrium data correlations can be extremely complex, especially when related to non-ideal multicomponent mixtures, and in order to handle such real life complex simulations, a commercial dynamic simulator with access to a physical property data-base often becomes essential. The approach in this text, is based, however, on the basic concepts of ideal behaviour, as expressed by Henry s law for gas absorption, the use of constant relative volatility values for distillation and constant distribution coeficients for solvent extraction. These have the advantage that they normally enable an explicit method of solution and avoid the more cumbersome iterative types of procedure, which would otherwise be required. Simulation examples in which more complex forms of equilibria are employed are STEAM and BUBBLE. 

Baptista M (2002) Comment on Explicit-solvent molecular dynamics simulation at constant pH Methodology and application to small amines . J Chem Phys 116 7766-7768. 

Borjesson U, Hiinenberger PH (2004) pH-dependent stability of a decalysine a-helix studied by explicit-solvent molecular dynamics simulations at constant pH. J Phys ChemB 108 13551-13559. 

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