Molecular dynamics simulations explicit solvent simulation

Noticeable differences in conformation of surfactant lipoprotein assessed via Monte Carte simulation with implicit solvent and molecular dynamics in explicit solvent were observed. 

Which of the two computer simulation methods is more efficient in accurately simulating (i) static and (ii) dynamic properties of a single polymer chain in dilute solution molecular dynamics with explicit solvent or Brownian dynamics without explicit solvent ... 

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 idea of a finite simulation model subsequently transferred into bulk solvent can be applied to a macromolecule, as shown in Figure 5a. The alchemical transformation is introduced with a molecular dynamics or Monte Carlo simulation for the macromolecule, which is solvated by a limited number of explicit water molecules and otherwise surrounded by vacuum. Then the finite model is transferred into a bulk solvent continuum... 

In the second group come molecular dynamics and Monte Carlo simulations, especially those where the solvent is modelled without being explicitly included. Their fourth class is the related supermolecule class, where we actually include solvent molecules in the simulation, and treat the entire array of molecules according to the rules of quantum mechanics or whatever. 

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. 

Quantitative models of solute-solvent systems are often divided into two broad classes, depending upon whether the solvent is treated as being composed of discrete molecules or as a continuum. Molecular dynamics and Monte Carlo simulations are examples of the former 8"11 the interaction of a solute molecule with each of hundreds or sometimes even thousands of solvent molecules is explicitly taken into account, over a lengthy series of steps. This clearly puts a considerable demand upon computer resources. The different continuum models,11"16 which have evolved from the work of Bom,17 Bell,18 Kirkwood,19 and Onsager20 in the pre-computer era, view the solvent as a continuous, polarizable isotropic medium in which the solute molecule is contained within a cavity. The division into discrete and continuum models is of course not a rigorous one there are many variants that combine elements of both. For example, the solute molecule might be surrounded by a first solvation shell with the constituents of which it interacts explicitly, while beyond this is the continuum solvent.16... 

TvaroSka, KoS r and Hricovini in this book). One way to account for the effect of solvent on conforxnation might be to represent the molecule without environmental influences, and then explicitly include the solvent or other environmental molecules in the calculation. While avoiding built-in influences of environment is a satisfying concept, it is difficult to obtain by experiment parameters that lack those influences. Several methods have been used to study solvation effects, including continuum descriptions (24) and the explicit treatment of solvent molecules in Monte Carlo and molecular dynamics simulation. 

It should be recalled that the calculation of solvent effects on optical activity presents some unique problems. A chiral solute induces a chiral structure of the surrounding solvent, even when the individual solvent molecules are achiral. This means that the solvent participates in the observed optical effect not only by a modification of the geometric structure and electronic density of the solute, but that part of the observed OR or circular dichroism arises from the chiral solvent shell rather than from the solute molecule as such. This is not accounted for by the PCM, and can be rendered only by an explicit quantum mechanical treatment of at least the first solvent shell, or preferably by molecular dynamics simulations. 

The main advantage of the MFA is that it permits one to dramatically reduce the computational requisites associated with the study of solvent effects. This allows one to focus attention on the solute description, and it consequently becomes possible to use calculation levels similar to those usually employed in the study of systems and processes in the gas phase. Furthermore, in the case of ASEP/MD this high level description of the solute is combined with a detailed description of the solvent structure obtained from molecular dynamics simulations. Thanks to these features ASEP/MD [8] enables the study of systems and processes where it is necessary to have simultaneously a good description of the electron correlation of the solute and the explicit consideration of specific solute-solvent interactions, such as for VIS-UV spectra [9] or chemical reactivity [10]. 

This method avoids the convergence and accuracy problems of molecular dynamics or Monte Carlo simulations of systems containing explicit solvent molecules, by evaluating the electrostatic free energy of just one solute conformation surrounded by a dielectric continuum, and by adding the surface term and an estimate of the loss of the configurational entropy upon binding.77... 

From a theoretical perspective, general force fields, being designed to reproduce the properties of large biological systems, might have difficulties in the simulation of small molecules. On the other hand, high-level ab initio calculations are possible only for a small number of conformations in vacuum or in the presence of implicit solvent, and prohibitively expensive for extended molecular dynamics or explicit... 

Solvent effects can significantly influence the function and reactivity of organic molecules.1 Because of the complexity and size of the molecular system, it presents a great challenge in theoretical chemistry to accurately calculate the rates for complex reactions in solution. Although continuum solvation models that treat the solvent as a structureless medium with a characteristic dielectric constant have been successfully used for studying solvent effects,2,3 these methods do not provide detailed information on specific intermolecular interactions. An alternative approach is to use statistical mechanical Monte Carlo and molecular dynamics simulation to model solute-solvent interactions explicitly.4 8 In this article, we review a combined quantum mechanical and molecular mechanical (QM/MM) method that couples molecular orbital and valence bond theories, called the MOVB method, to determine the free energy reaction profiles, or potentials of mean force (PMF), for chemical reactions in solution. We apply the combined QM-MOVB/MM method to... 

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