Neighbour lists

There are no fixed rules that determine how much larger the neighbour list cutoff should be than the non-bonded cutoff. Clearly there will be a trade-off between the size of the cutoff and the frequency at which the neighbour hst must be updated the larger the difference, the less frequently will the neighbour list have to be updated. There may also be storage implications if the list is too large. 

Pointer and neighbour arrays can be used to implement the Verlet neighbour list. 

Table 7.1 presents us with something of a dilemma. We would obviously desire to explore i much of the phase space as possible but this may be compromised by the need for a sma time step. One possible approach is to use a multiple time step method. The underlyir rationale is that certain interactions evolve more rapidly with rime than other interaction The twin-range method (Section 6.7.1) is a crude type of multiple time step approach, i that interactions involving atoms between the lower and upper cutoff distance remai constant and change only when the neighbour list is updated. However, this approac can lead to an accumulation of numerical errors in calculated properties. A more soph sticated approach is to approximate the forces due to these atoms using a Taylor seri< expansion [Streett et al. 1978] ... 

Whittle M, GiUet VJ, Willett P, Alex A, Losel J. (2004) Enhancing the Effectiveness of Virtual Screening by Fusing Nearest-Neighbour Lists A Comparison of Similarity Coefficients. J. Chem. Inf. Comp. Set. 44 1840-1848. 

Weiser J, Weiser AA, Shenkin PS, Still WC (1998) Neighbour-list reduction optimization for computation of molecular van der Waals and solvent accessible surface areas, I Comput Chem, 19 797-808... 

If the pair have at least Almin of their top-AT nearest neighbours in common and each is in the top-Al nearest-neighbour list ofthe other, then replace all occurrences ofthe Label entry for/with the Label entry for/. 

Z. A. Rycerz, Comput. Phys. Commun., 60, 297 (1990). Acceleration of Molecular Dynamics Simulation of Order N with Neighbour List. 

A. A. Chiavlo and P. G. Debenedetti, Comput. Phys. Commun., 64, 15 (1991). On the Performance of an Automated Verier Neighbour List Algorithm for Large Systems on a Vector Processor. 

D. Fincham and P. J. Mitchell, Mol. Simulation, 7, 135 (1991). Multicomputer Molecular Dynamics Simulation Using Distributed Neighbour Lists. 

Neighbour list, in force field methods, 43 Newton-Raphson (NR) optimization, 318,... 

Thompson S M 1983. Use of Neighbour Lists in Molecular Dynamics. CCP5 Quarterly 8 20-28. van Gunsteren W F and H J C Berendsen 1986. GROMOS User Guide. 

At the end of these two loops, the total force on each atom is known. A consequence of the fact that the force between the two atoms is equal and opposite is that the neighbour list for each atom need only contain those atoms with a higher number as the force on an atom due to interactions with lower numbered atoms will be calculated earlier in the loop. This organisation of the neighbour list contrasts with the structure used for Monte Carlo simulations, where all the neighbours of each atom (with both lower and higher indices) must be stored. 

Conformations can thus be placed in clusters and clusters fused together (because any two individual elements satisfy the two criteria) without any hierarchical relationships. The Jarvis-Patrick method can also be extended to take account not only of the number of nearest neighbours but also the position of each conformation within the neighbour list. In addition, it is possible to require that a molecule s nearest neighbours must be within some defined distance. This ensures that the nearest neighbours of each conformation are not too dissimilar. 

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