Optimization techniques for parallel molecular dynamics using domain decomposition

The reorientation dynamics of local tangent vectors of chains in isotropic amorphous melts containing semiflexible model polymers was studied by molecular dynamics simulations. The reorientation is strongly influenced both by the local chain stiffness and by the overall chain length. It takes place by two different subsequent processes: A shorttime non-exponential decay and a long-time exponential reorientation arising from the relaxation of medium-size chain segments. Both processes depend on stiffness and chain length. The strong influence of the chain length on the chain dynamics is in marked contrast to its negligible effect on the static structure of the melt. The local structure shows only a small dependence on the stiffness, and is independent of chain length. Calculated correlation functions related to double-quantum NMR experiments are in qualitative agreement with experiments on entangled melts. A plateau is observed in the dependence of segment reorientation on the mean-squared displacement of the corresponding chain segments. This plateau confirms, on one hand, the existence of reptation dynamics. On the other hand, it shows how the reptation 1 picture has to be adapted if, instead of fully flexible chains, semirigid chains are considered.

show abstract

“…23. Throughout this work, reduced units are used with mass m, bead diameter σ, and the strength of the WCA potential ǫ set to unity.…”

Section: Model and Computational Detailsmentioning

confidence: 99%

Local Reorientation Dynamics of Semiflexible Polymers in the Melt

2000

View full text Add to dashboard Cite

show abstract

“…measure is independent of the actual implementation of the algorithms and is typically used in previous works to show their potential efficiency. For instance, the strategy of partitioning the domain using cells of edge length to half the cutoff [23,26] computes a 58% of the number of distances computed by the plain CLL, and S-CLL reduces this ratio to a 26%. As shown in the table, as far as the size of the rigid clusters is large, the Rigid-CLL algorithm performs remarkably better than the standard CLL algorithm reducing the number of distances actually computed to a ratio similar or even lower than those of previous works.…”

Section: Methodsmentioning

confidence: 99%

“…Many variants of the CLL algorithm have been proposed to improve its performance. One possible approximation is to use smaller cells [23,26]. The problems with this approach are the large memory requirements and the increase of the number of neighboring cells to be checked for each atom, which can lead to computational inefficiencies, particularly due to the high percentage of empty cells.…”

Section: Introductionmentioning

confidence: 99%

“…In these cases, though, any gain obtained comes at the extra cost of the sorting process. The CLL algorithm can also be sped up by parallelizing the nearest-neighbor detection [16,22,26,30], sometimes resorting to special hardware which can be either not generally available [9] or too specialized, avoiding the use of optimal CLL algorithms [12]. Finally, another approach to reduce the cost of the CLL algorithm is to group closely connected particles [25].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

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

2011

View full text Add to dashboard Cite

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.

show abstract

“…In the spatial decomposition methods 13,16,17,[35][36][37][38][39][40][41][42][43][44][45][46][47][48][49][50][51][52][53][54] (also referred to as domain decomposition or geometric methods), each processor is associated with a fixed block of space throughout the course of the simulation. During a given MD time step, the processor is responsible for calculating the forces experienced by all atoms currently residing within its own block and updating their respective positions, but atoms may move from one block (and thus one processor) to another over the course of the simulation.…”

Section: Standard Methods For Parallelizing MD Simulationsmentioning

confidence: 99%

A fast, scalable method for the parallel evaluation of distance‐limited pairwise particle interactions

2005

View full text Add to dashboard Cite

Classical molecular dynamics simulations of biological macromolecules in explicitly modeled solvent typically require the evaluation of interactions between all pairs of atoms separated by no more than some distance R, with more distant interactions handled using some less expensive method. Performing such simulations for periods on the order of a millisecond is likely to require the use of massive parallelism. The extent to which such simulations can be efficiently parallelized, however, has historically been limited by the time required for interprocessor communication. This article introduces a new method for the parallel evaluation of distance-limited pairwise particle interactions that significantly reduces the amount of data transferred between processors by comparison with traditional methods. Specifically, the amount of data transferred into and out of a given processor scales as O(R 3/ 2 p Ϫ1/ 2 ), where p is the number of processors, and with constant factors that should yield a substantial performance advantage in practice.

show abstract

Optimization techniques for parallel molecular dynamics using domain decomposition

Cited by 46 publications

References 26 publications

Local Reorientation Dynamics of Semiflexible Polymers in the Melt

Local Reorientation Dynamics of Semiflexible Polymers in the Melt

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

A fast, scalable method for the parallel evaluation of distance‐limited pairwise particle interactions

Contact Info

Product

Resources

About