Parallel programming library for molecular dynamics simulations

Trobec, Roman; Sterk, Marjan; Praprotnik, Matej; Janežič, Dušanka

doi:10.1002/qua.10742

Cited by 8 publications

(10 citation statements)

References 21 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…It was shown that SISM offers better performances in comparison with LFV for both sequential and parallel implementation. SISM performs in parallel as LFV which means the speed up is gained due to a longer time step, which can be used by SISM 20–22.…”

Section: Discussionmentioning

confidence: 99%

Symplectic molecular dynamics integration using normal mode analysis

Janežič

Praprotnik

2001

Int J of Quantum Chemistry

View full text Add to dashboard Cite

ABSTRACT:The split integration symplectic method (SISM) for molecular dynamics (MD) integration using normal mode analysis based on a factorization of the Liouville propagator is presented. This approach is quite distinct from others that use fractional-step methods, owing to the analytical treatment of high-frequency motions. The method involves splitting the total Hamiltonian of the system into a harmonic part and the remaining part. Then the Hamilton equations are solved using a second-order generalized leapfrog integration scheme in which the purely harmonic Hamiltonian (which represents the main contribution of the chemical bonds and angles) is treated analytically, i.e., independent of the step size of integration, by a normal mode analysis that is carried out only once, at the beginning of calculation. The whole integration step combines analytical evolution of the harmonic part of the Hamiltonian with a correction arising from the remaining part. The proposed algorithm requires only one force evaluation per integration step. The algorithm was tested on a simple system of linear chain molecules. Results demonstrate the method makes possible the integration of the MD equations over larger time steps without loss of stability while being economical in computer time.

show abstract

Section: Discussionmentioning

confidence: 99%

Symplectic molecular dynamics integration using normal mode analysis

Janežič

Praprotnik

2001

Int J of Quantum Chemistry

View full text Add to dashboard Cite

show abstract

“…10 Since the processors must frequently exchange data and each simulation time step is dependent on the previous step, load balancing and fast low-latency communication is crucial for obtaining good computational performance. 11,12 Most recent parallel computers are often built as computing clusters, many of them Beowulf-type clusters of personal computers (PCs) 13 connected into a separate network serving as the primary processor interconnection. 14 The processors cannot directly access the memory on other PCs, meaning that PC clusters have a distributed-memory Multiple Instruction Multiple Data (MIMD) architecture.…”

Section: Introductionmentioning

confidence: 99%

“…13 Programs written for such a parallel architecture must use message passing for transferring all of the data among processors and care must be taken to reduce the communication time. 11,12,15 Besides parallelization, specialized processors may also be used to increase computational speed. 16,17 The MDGRAPE-2 (Molecular Dynamics Gravity Pipeline) processor is designed for the fast calculation of nonbonding interactions in MD simulations.…”

Section: Introductionmentioning

confidence: 99%

Symplectic Molecular Dynamics Simulations on Specially Designed Parallel Computers

Borštnik

Janežič

2005

J. Chem. Inf. Model.

View full text Add to dashboard Cite

We have developed a computer program for molecular dynamics (MD) simulation that implements the Split Integration Symplectic Method (SISM) and is designed to run on specialized parallel computers. The MD integration is performed by the SISM, which analytically treats high-frequency vibrational motion and thus enables the use of longer simulation time steps. The low-frequency motion is treated numerically on specially designed parallel computers, which decreases the computational time of each simulation time step. The combination of these approaches means that less time is required and fewer steps are needed and so enables fast MD simulations. We study the computational performance of MD simulation of molecular systems on specialized computers and provide a comparison to standard personal computers. The combination of the SISM with two specialized parallel computers is an effective way to increase the speed of MD simulations up to 16-fold over a single PC processor.

show abstract

“…In some problems where a significant amount of global communication is needed, e.g. molecular dynamics, , optimal performance of intracluster communication is particularly important.…”

Section: Introductionmentioning

confidence: 99%

Biomedical Simulation of Heat Transfer in a Human Heart

Sterk

Trobec

2005

J. Chem. Inf. Model.

View full text Add to dashboard Cite

Theory and practical experiences from numerical simulations of heat transfer in the field of medicine are presented in this paper. The cooling of a human heart during surgery was taken as an illustrative example. All phases of the simulation process are described starting with the construction of an irregularly shaped 3-dimensional model. The mathematical model is based on diffusion and Navier-Stokes equations. The system of partial differential equations is solved by finite difference approximation using an explicit time-stepping scheme to obtain the time evolution of the solution for the complete simulated interval, which is typically 1 h. A typical domain is composed of several million voxels; therefore, the program was parallelized to speed up the simulation. A speed-up of 8.2 was obtained on 16 processors in a Linux cluster.

show abstract

Parallel programming library for molecular dynamics simulations

Cited by 8 publications

References 21 publications

Symplectic molecular dynamics integration using normal mode analysis

Symplectic molecular dynamics integration using normal mode analysis

Symplectic Molecular Dynamics Simulations on Specially Designed Parallel Computers

Biomedical Simulation of Heat Transfer in a Human Heart

Contact Info

Product

Resources

About