Molecular dynamics electrostatic interactions

The molecule is often represented as a polarizable point dipole. A few attempts have been performed with finite size models, such as dielectric spheres [64], To the best of our knowledge, the first model that joined a quantum mechanical description of the molecule with a continuum description of the metal was that by Hilton and Oxtoby [72], They considered an hydrogen atom in front of a perfect conductor plate, and they calculated the static polarizability aeff to demonstrate that the effect of the image potential on aeff could not justify SERS enhancement. In recent years, PCM has been extended to systems composed of a molecule, a metal specimen and possibly a solvent or a matrix embedding the metal-molecule system in a molecularly shaped cavity [62,73-78], In particular, the molecule was treated at the Hartree-Fock, DFT or ZINDO level, while for the metal different models have been explored for SERS and luminescence calculations, metal aggregates composed of several spherical particles, characterized by the experimental frequency-dependent dielectric constant. For luminescence, the effects of the surface roughness and the nonlocal response of the metal (at the Lindhard level) for planar metal surfaces have been also explored. The calculation of static and dynamic electrostatic interactions between the molecule, the complex shaped metal body and the solvent or matrix was done by using a BEM coupled, in some versions of the model, with an IEF approach. 

Procacci P, Darden T A, Paci E and Marchi M 1997 ORAC a molecular dynamics program to simulate complex molecular systems with realistic electrostatic interactions J. Comput. Chem. 18 1848-62... 

Procacci, P., Darden, T., Marchi, M., A very fast molecular dynamics method to simulate biomolecular systems with realistic electrostatic interactions. J. Phys. Chem. 100 (1996) 10464-10468. 

Belhadj,M., Alper, H.A., Levy, R.M. Molecular dynamics simulations of wa ter with Ewald summation for the long-range electrostatic interactions. Chem. Phys. Lett. 179 (1991) 13-20. 

M. Eichinger, H. Grubmiiller, H. Heller, and P. Tavan. FAMUSAMM An algorithm for rapid evaluation of electrostatic interaction in molecular dynamics simulations. J. Comp. Chem., 18 1729-1749, 1997. 

Ligand-Protein Interactions The energy of formation of ligand-protein contacts can be computed as a sum of non-bonded (Lennard-Jones and electrostatic) terms similar to those used in a molecular dynamics simulation. 

In an atomic level simulation, the bond stretch vibrations are usually the fastest motions in the molecular dynamics of biomolecules, so the evolution of the stretch vibration is taken as the reference propagator with the smallest time step. The nonbonded interactions, including van der Waals and electrostatic forces, are the slowest varying interactions, and a much larger time-step may be used. The bending, torsion and hydrogen-bonding forces are treated as intermediate time-scale interactions. 

Parallel molecular dynamics codes are distinguished by their methods of dividing the force evaluation workload among the processors (or nodes). The force evaluation is naturally divided into bonded terms, approximating the effects of covalent bonds and involving up to four nearby atoms, and pairwise nonbonded terms, which account for the electrostatic, dispersive, and electronic repulsion interactions between atoms that are not covalently bonded. The nonbonded forces involve interactions between all pairs of particles in the system and hence require time proportional to the square of the number of atoms. Even when neglected outside of a cutoff, nonbonded force evaluations represent the vast majority of work involved in a molecular dynamics simulation. 

In periodic boimdary conditions, one possible way to avoid truncation of electrostatic interaction is to apply the so-called Particle Mesh Ewald (PME) method, which follows the Ewald summation method of calculating the electrostatic energy for a number of charges [27]. It was first devised by Ewald in 1921 to study the energetics of ionic crystals [28]. PME has been widely used for highly polar or charged systems. York and Darden applied the PME method already in 1994 to simulate a crystal of the bovine pancreatic trypsin inhibitor (BPTI) by molecular dynamics [29]. 

Before running a molecular dynamics simulation with solvent and a molecular mechanics method, choose the appropriate dielectric constant. You specify the type and value of the dielectric constant in the Force Field Options dialog box. The dielectric constant defines the screening effect of solvent molecules on nonbonded (electrostatic) interactions. 

The concentration of salt in physiological systems is on the order of 150 mM, which corresponds to approximately 350 water molecules for each cation-anion pair. Eor this reason, investigations of salt effects in biological systems using detailed atomic models and molecular dynamic simulations become rapidly prohibitive, and mean-field treatments based on continuum electrostatics are advantageous. Such approximations, which were pioneered by Debye and Huckel [11], are valid at moderately low ionic concentration when core-core interactions between the mobile ions can be neglected. Briefly, the spatial density throughout the solvent is assumed to depend only on the local electrostatic poten-... 

A molecular dynamics force field is a convenient compilation of these data (see Chapter 2). The data may be used in a much simplified fonn (e.g., in the case of metric matrix distance geometry, all data are converted into lower and upper bounds on interatomic distances, which all have the same weight). Similar to the use of energy parameters in X-ray crystallography, the parameters need not reflect the dynamic behavior of the molecule. The force constants are chosen to avoid distortions of the molecule when experimental restraints are applied. Thus, the force constants on bond angle and planarity are a factor of 10-100 higher than in standard molecular dynamics force fields. Likewise, a detailed description of electrostatic and van der Waals interactions is not necessary and may not even be beneficial in calculating NMR strucmres. 

Approximating the intermoleculai interactions to only include two-body effects, e.g. electrostatic forces are only calculated between pairs of fixed atomic chai ges in force field techniques. Or the discrete interactions between molecules may be treated only in an average fashion, by using Langevin dynamics instead of molecular dynamics. 

Thus the formation of tilted analogues of the smectic A phases, i.e. monolayer Cl and bilayer C2, is possible for mesogens with relatively large electric quadrupoles. In the case of strongly sterically asymmetric molecules (e.g., zigzag shaped or dumbell shaped molecules, Fig. 3b) these quadrupolar interactions may be steric in origin. From this point of view observation of molecular tilt in the molecular dynamics simulations for a one-layer film of DOBAMBC in the absence of electrostatic interactions is not so surprising [106]. 

When the MM subsystem is being optimized, or a molecular dynamics simulation is being carried out on the MM subsystem, the QM/MM electrostatic interactions are approximated with fixed point charges on the QM atoms which are fitted to reproduce the electrostatic potential (ESP) of the QM subsystem [37],... 

---