Solvent explicit

The interaction with the solvent is of similar importance as the intramolecuiar energy contributions and a correct representation of the solvent is therefore es.sential. If an explicit solvent description is chosen, averaging over many different solvent configurations is necessary in order to obtain converged statistical averages. Advantageous in this respect is describing the solvent as... 

A second idea to save computational time addresses the fact that hydrogen atoms, when involved in a chemical bond, show the fastest motions in a molecule. If they have to be reproduced by the simulation, the necessary integration time step At has to be at least 1 fs or even less. This is a problem especially for calculations including explicit solvent molecules, because in the case of water they do not only increase the number of non-bonded interactions, they also increase the number of fast-moving hydrogen atoms. This particular situation is taken into account... 

By using an effective, distance-dependent dielectric constant, the ability of bulk water to reduce electrostatic interactions can be mimicked without the presence of explicit solvent molecules. One disadvantage of aU vacuum simulations, corrected for shielding effects or not, is the fact that they cannot account for the ability of water molecules to form hydrogen bonds with charged and polar surface residues of a protein. As a result, adjacent polar side chains interact with each other and not with the solvent, thus introducing additional errors. 

You can use two types of dielectric fun ction s a con stan t an d a dis-tan ce-depen den t dielectric. Use con stan t dielectric for in i- floio systems and for molecular systems wfith explicit solvent molecules. 

Also use constant dielectric Tor MM+aiul OPLS ciilciilatimis. Use the (lislance-flepeiident dielecinc for AMBER and BlO+to mimic the screening effects of solvation when no explicit solvent molecules are present. The scale factor for the dielectric permittivity, n. can vary from 1 to H(l. IlyperChem sets tt to 1. .5 for MM-r. Use 1.0 for AMBER and OPLS. and 1.0-2..5 for BlO-r. 

The primary problem with explicit solvent calculations is the significant amount of computer resources necessary. This may also require a significant amount of work for the researcher. One solution to this problem is to model the molecule of interest with quantum mechanics and the solvent with molecular mechanics as described in the previous chapter. Other ways to make the computational resource requirements tractable are to derive an analytic equation for the property of interest, use a group additivity method, or model the solvent as a continuum. 

The most accurate calculations are those that use a layer of explicit solvent molecules surrounded, in turn, by a continuum model. This adds the additional... 

A layer of explicit solvent molecules surrounded by a continuum description for the highest possible accuracy. 

PCM when quantum mechanics is necessary, but explicit solvent simulations are too CPU-intensive. 

Explicit solvent methods. Monte Carlo methods are somewhat more popular than molecular dynamics methods. 

As for the dielectric constant, when explicit solvent molecules are included in the calculations, a value of 1, as in vacuum, should be used because the solvent molecules themselves will perform the charge screening. The omission of explicit solvent molecules can be partially accounted for by the use of an / -dependent dielectric, where the dielectric constant increases as the distance between the atoms, increases (e.g., at a separation of 1 A the dielectric constant equals 1 at a 3 A separation the dielectric equals 3 and so on). Alternatives include sigmoidal dielectrics [80] however, their use has not been widespread. In any case, it is important that the dielectric constant used for a computation correspond to that for which the force field being used was designed use of alternative dielectric constants will lead to improper weighting of the different electrostatic interactions, which may lead to significant errors in the computations. 

C. Explicit Solvent Models and the Importance of Balancing the External Interactions... 

Another way is to reduce the magnitude of the problem by eliminating the explicit solvent degrees of freedom from the calculation and representing them in another way. Methods of this nature, which retain the framework of molecular dynamics but replace the solvent by a variety of simplified models, are discussed in Chapters 7 and 19 of this book. An alternative approach is to move away from Newtonian molecular dynamics toward stochastic dynamics. 

In finite boundary conditions the solute molecule is surrounded by a finite layer of explicit solvent. The missing bulk solvent is modeled by some form of boundary potential at the vacuum/solvent interface. A host of such potentials have been proposed, from the simple spherical half-harmonic potential, which models a hydrophobic container [22], to stochastic boundary conditions [23], which surround the finite system with shells of particles obeying simplified dynamics, and finally to the Beglov and Roux spherical solvent boundary potential [24], which approximates the exact potential of mean force due to the bulk solvent by a superposition of physically motivated tenns. 

It is possible to go beyond the SASA/PB approximation and develop better approximations to current implicit solvent representations with sophisticated statistical mechanical models based on distribution functions or integral equations (see Section V.A). An alternative intermediate approach consists in including a small number of explicit solvent molecules near the solute while the influence of the remain bulk solvent molecules is taken into account implicitly (see Section V.B). On the other hand, in some cases it is necessary to use a treatment that is markedly simpler than SASA/PB to carry out extensive conformational searches. In such situations, it possible to use empirical models that describe the entire solvation free energy on the basis of the SASA (see Section V.C). An even simpler class of approximations consists in using infonnation-based potentials constructed to mimic and reproduce the statistical trends observed in macromolecular structures (see Section V.D). Although the microscopic basis of these approximations is not yet formally linked to a statistical mechanical formulation of implicit solvent, full SASA models and empirical information-based potentials may be very effective for particular problems. 

Over the next decade a number of efforts were made to apply MD simulations using explicit solvent representations to DNA. A number of these calculations were performed... 

Initial atomistic calculations on nucleic acids were perfonned in the absence of an explicit solvent representation, as discussed earlier. To compensate for this omission, various... 

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