Dielectric distance-dependent

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. 

In this model of electrostatic in teraction s, two atoms (i and j) have poin t charges tq and qj. The magnitude of the electrostatic energy (V[. , [ ) varies inversely with the distance between the atoms, Rjj. fh e effective dielectric constant is . For in vacuo simulations or simulation s with explicit water rn olecules, the den om in a tor equals uRjj, In some force fields, a distance-dependent dielectric, where the denominator is uRjj Rjj, represen is solvent implicitly. 

Li) he so-called distance-dependent dielectric models. The simplest implementation of a dis-i.iiice-dependent dielectric is to make the relative permittivity proportional to the distance. Tine interaction energy between two charges qi and qj then becomes ... 

Use a constant dielectric of 1.0 with TIP3P water molecules in a periodic box. Because of the parameterization of TIP3P molecules, using a distance-dependent dielectric or a value other than 1.0 gives unnatural results. 

A distance-dependent dielectric constant is commonly used to mimic the effect of solvent in molecular mechanics calculations, in the absence of explicit water molecules. 

You can use two types of dielectric functions a constant and a distance-dependent dielectric. Use constant dielectric for in vacuo systems and for molecular systems with explicit solvent molecules. 

Also use constant dielectric for MM+ and OPLS calculations. Use the distance-dependent dielectric for AMBER and BlO-t to mimic the screening effects of solvation when no explicit solvent molecules are present. The scale factor for the dielectric permittivity, 8, can vary from 1 to 80. HyperChem sets 8 to 1.5 for MM-t. Use 1.0 for AMBER and OPLS, and 1.0-2.5 for BlO-t. 

What is the relationship between a constant dielectric and a distance dependant dielectric for pseudo-vacuum simulations ... 

Macroscopic models have been developed that describe the protein and the water as macroscopic dielectric materials. In their simplest form these models use a distance-independent dielectric function, i.e. a simple Coulomb interaction. Others may apply a distance-dependent dielectric function. The more detailed implementatiorrs include a descriptions of the protein-solvent botmdary in terms of solvent accessibihty and ionic-strength effects (Gilson and Honig, 1988). 

Models have been described in the literature for AP-B [53] and Bunodosoma granulifera toxins II (Bg II) [26]. The AP-B model was derived from the structure of Sh I using energy minimization and the Bg II model from that of BDS I using energy minimization and 10 ps of dynamics. In both cases the calculations appear to have been carried out for the molecule in vacuo without the use of a distance-dependent dielectric, under which conditions the positions of the charged side chains on the surface are likely to be distorted. Visual comparison of the model of AP-B [53] with the experimentally determined solution structure [47] indicates significant differences in side-chain orientations. 

Places the Langevin dipoles at grid points. I The (1 +r0) term is a distance dependent dielectric constant for the non iterative LD procedure (See references 4). 

The molecule preparation step includes also conformational expansion using a torsional search or a combined Monte Carlo Multiple Minimum/Low Mode search. During the search, the intramolecular hydrogen bonds are not considered. Molecules can be minimized, OPLS-2005 or MMFF force fields [86, 87] are available, and also two continuum solvation models (distance-dependent dielectric or GB/SA). A double criterion is used to eliminate redundant conformations it uses distances between pairs of corresponding atoms within a 1 kcal moh1 energy window. 

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