Electrostatic simulations

Figure 7-2. Properties of CAII active site in the COHH state (zinc-bound hydroxide and protonated His 64). (a) Superposition of a few key residues from two stochastic boundary SCC-DFTB/MM simulations with the X-ray structure [87] (colored based on atom-types) the two sets of simulations did not have any cut-off for the electrostatic interactions between SCC-DFTB and MM atoms but used different treatments for the electrostatic interactions among MM atoms group-based extended electrostatics (in yellow) and atom-based force-shift cut-off (in green). Extended electrostatics simulations sampled configurations with the protonated His 64 too close to the zinc moiety while force-shift simulations consistently sampled the out configuration of His 64 in multiple trajectories, (b) Statistics for productive water-bridges (only from two and four shown here) between the zinc bound water and His 64 with different electrostatics protocols...

Figure 3.34 (a) Geometry and (b) electrostatic simulation results of the extended-body, high-voltage package. 

Therefore, a model was developed for a full size IPMC based on Nafion 117 coated with thin layer of platinum [Pugal et al. (2010b)]. The mass transfer and electrostatic simulations are modeled for the backbone polymer. All simulations were done for an IPMC strip of 180 /Ltm thick polymer coated with 5 /um thick platinum, in a cantilever configuration — one end of the strip is fixed. 

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Procacci P, March M and Martyna G J 1998 Electrostatic calculations and multiple time scales in molecular dynamics simulation of flexible molecular systems J. Chem. Phys. 108 8799-803... 

Madura J D, Davis M E, Gilson, M K, Wade R C, Luty B A and McCammon J A 1994 Biological applications of electrostatic calculations and Brownian dynamics simulations Rev. Comput. Chem. 5 229-67... 

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. 

Smith, P.E and Van Gunsteren, W.F. Methc electrostatic forces in computer simulation ... 

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. 

The first term represents the forces due to the electrostatic field, the second describes forces that occur at the boundary between solute and solvent regime due to the change of dielectric constant, and the third term describes ionic forces due to the tendency of the ions in solution to move into regions of lower dielectric. Applications of the so-called PBSD method on small model systems and for the interaction of a stretch of DNA with a protein model have been discussed recently ([Elcock et al. 1997]). This simulation technique guarantees equilibrated solvent at each state of the simulation and may therefore avoid some of the problems mentioned in the previous section. Due to the smaller number of particles, the method may also speed up simulations potentially. Still, to be able to simulate long time scale protein motion, the method might ideally be combined with non-equilibrium techniques to enforce conformational transitions. 

Madura et al. 1995] Madura, J.D., Briggs, J.M., Wade, R.C., Davis, M.E., Luty, B.A., Ilin, A., Antosiewicz, J., Gilson, M.K., Bagheri, B., Scott, L.R., McCammon, J.A. Electrostatics and Diffusion of Molecules in Solution Simulations with the University of Houston Brownian Dynamics Program. Comp. Phys. Comm. 91 (1995) 57-95... 

B. A. Luty, I. G. Tironi, and W. F. van Gunsteren. Lattice-sum methods for calculating electrostatic interactions in molecular simulations. J. Chem. Phys., 103 3014-3021, 1995. 

U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee, and L. G. Pedersen. The smooth particle mesh ewald method. J. Chem. Phys., 103 8577, 1995. Brock A. Luty, Ilario G. Tironi, and Wilfried F. van Gunsteren. Lattice-sum methods for calculating electrostatic interactions in molecular simulations. J. Chem. Phys., 103 3014-3021, 1995. 

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. 

J. A. Electrostatics and disffusion of molecules in solution simulations with the university of houston brownian dynamics program. Comp. Phys. Commun. 91 (1996) 57-95. 

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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. 

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. 

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