Rigid‐CLL: Avoiding constant‐distance computations in cell linked‐lists algorithms

Abstract

Many of the existing molecular simulation tools require the efficient identification of the set of non-bonded interacting atoms. This is necessary, for instance, to compute the energy values or the steric contacts between atoms. Cell linked-lists can be used to determine the pairs of atoms closer than a given cutoff distance in asymptotically optimal time. Despite this long-term optimality, many spurious distances are anyway computed with this method. Therefore, several improvements have been proposed, most of them aiming to refine the volume of influence for each atom. Here, we suggest a different improvement strategy based on avoiding to fill cells with those atoms that are always at a constant distance of a given atom. This technique is particularly effective when large groups of the particles in the simulation behave as rigid bodies as it is the case in simplified models considering only few of the degrees of freedom of the molecule. In these cases, the proposed technique can reduce the number of distance computations by more than one order of magnitude, as compared with the standard cell linked-list technique. The benefits of this technique are obtained without incurring in additional computation costs, because it carries out the same operations as the standard cell linked-list algorithm, although in a different order. Since the focus of the technique is the order of the operations, it might be combined with existing improvements based on bounding the volume of influence for each atom.

Exploring the energy landscapes of flexible molecular loops using higher‐dimensional continuation

“…In the future, we aim to exploit the symmetries that appear in many problems [53] and to speed up the steric clash detection [52]. These improvements might help to reduce the computational burden of the approach in more challenging problems.…”

Investigating the Formation of Structural Elements in Proteins Using Local Sequence-Dependent Information and a Heuristic Search Algorithm

“…The test of collision-free states is computed using a variant of the classical cell linked-list (CLL) algorithm [46]. A pair of non-bonded (pseudo-)atoms is considered to be in collision if their distance is less than 65% of the sum of their radii.…”