Nonbonded methods

In nonbonded methods, the metal ion is not formally connected to the ligand donor atoms and the metal-dependent interactions present in bonded methods are not included. There are no explicit M-L bonds, M-L-X and L-M-L angles, or M-L-X-X and L-M-L-X torsional interactions. Instead the metal-ligand complex is modeled with a collection of pairwise electrostatic and van der Waals interactions between the metal and all ligand atoms, i.e., with M-L and M-X interactions. 

A novel nonbonded method has been used to model the TT-bound ligands of cyclopentadienyl sandwich compounds. ... 

In LN, the bonded interactions are treated by the approximate linearization, and the local nonbonded interactions, as well as the nonlocal interactions, are treated by constant extrapolation over longer intervals Atm and At, respectively). We define the integers fci,fc2 > 1 by their relation to the different timesteps as Atm — At and At = 2 Atm- This extrapolation as used in LN contrasts the modern impulse MTS methods which only add the contribution of the slow forces at the time of their evaluation. The impulse treatment makes the methods symplectic, but limits the outermost timestep due to resonance (see figures comparing LN to impulse-MTS behavior as the outer timestep is increased in [88]). In fact, the early versions of MTS methods for MD relied on extrapolation and were abandoned because of a notable energy drift. This drift is avoided by the phenomenological, stochastic terms in LN. 

Formally, we describe the LN method with the above force splitting below for the triplet protocol At, Atm, At. The fast, medium, and slow force components are distinguished by subscripts we take the medium forces as those nonbonded interactions within a 6 A region. 

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. 

Methods of decomposing the nonbonded force evaluation fall into two classes, spatial decomposition [15] in which atoms and their interactions are divided among processors based on their coordinates, and force-matrix decomposition [16] in which the calculation of the interaction between a pair of atoms is assigned to a processor without considering the location of either atom (Fig. 1). Spatial decomposition scales better to large numbers of... 

Ding H-Q, N Karasawa and W A Goddard III 1992a. Atomic Level Simulations on a Milhon Particles The Cell Multipole Method for Coulomb and London Nonbonding Interactions. Journal of Chemical Physics 97 4309-4315. 

I J, J C Cole, J P M Lommerse, R S Rowland, R Taylor and M L Verdonk 1997. Isostar A Libraij )f Information about Nonbonded Interactions. Journal of Computer-Aided Molecular Design 11 525-531. g G, W C Guida and W C Still 1989. An Internal Coordinate Monte Carlo Method for Searching lonformational Space. Journal of the American Chemical Scociety 111 4379-4386. leld C and A J Collins 1980. Introduction to Multivariate Analysis. London, Chapman Hall, ig C-W, R M Cooke, A E I Proudfoot and T N C Wells 1995. The Three-dimensional Structure of 1 ANTES. Biochemistry 34 9307-9314. 

Most of the methods proposed include a van der Waals term for describing nonbonded interactions between atoms in the two regions. This is usually represented by a Leonard-Jones 6-12 potential of the form... 

Arelatively simple method for alleviating some of the nonphysical behaviors caused by imposing a nonbonded cutoff is to use a potential switching function (equation 14). 

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. 

HyperChem supplements the standard MM2 force field (see References on page 106) by providing additional parameters (force constants) using two alternative schemes (see the second part of this book. Theory and Methods). This extends the range of chemical compounds that MM-t can accommodate. MM-t also provides cutoffs for calculating nonbonded interactions and periodic boundary conditions. 

Use nonbonded (NB) tmncation methods to reduce size of NB pairHst it is a dominating term in the calculation. It is important to remember the pairHst i A/, consider tmncation of NBs at 100—120 nm (10—12E), and to experiment with electrostatic cutoffs independentiy of van der Waals. 

Radiographic. Radiography is an exceUent nondestmctive test (NDT) method for evaluating the bond of Al—steel electrical and Al—Al—steel stmctural transition joints. It provides the capabiHty of precisely and accurately defining all nonbond and flat-bond areas of the Al—steel interface, regardless of size or location (see Surface and interface analysis). 

A. M. Mathiowetz, A. Jain, N. Karasawa, W. A. Goddard III. Protein simulations using techniques suitable for very large systems the cell multipole method for nonbond interactions and the Newton-Euler inverse mass operator method for internal coordinate dynamics. CN 8921. Proteins 20 221, 1994. 

See also Energy minimization methods computer program for, 130-132 Nonbonded interactions, 56,61 Normal modes analysis, 117-119 computer program for, 132-134... 

In a similar way the potential constant method as described here allows the simultaneous vibrational analysis of systems which differ in other strain factors. Furthermore, conformations and enthalpies (and other properties see Section 6.5. for examples) may be calculated with the same force field. For instance, vibrational, conformational, and energetic properties of cyclopentane, cyclohexane and cyclodecane can be analysed simultaneously with a single common force field, despite the fact that these cycloalkanes involve different distributions of angle and torsional strain, and of nonbonded interactions 8, 17). This is not possible by means of conventional vibrational spectroscopic calculations. 

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