Ändra sökning
RefereraExporteraLänk till posten
Permanent länk

Direktlänk
Referera
Referensformat
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Annat format
Fler format
Språk
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Annat språk
Fler språk
Utmatningsformat
  • html
  • text
  • asciidoc
  • rtf
A comparison of the Spectral Ewald and Smooth Particle Mesh Ewald methods in GROMACS
KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.), Numerisk analys, NA.
KTH, Centra, Science for Life Laboratory, SciLifeLab.ORCID-id: 0000-0002-7498-7763
KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.), Numerisk analys, NA.ORCID-id: 0000-0002-4290-1670
(Engelska)Manuskript (preprint) (Övrigt vetenskapligt)
Abstract [en]

The smooth particle mesh Ewald (SPME) method is an FFT based methodfor the fast evaluation of electrostatic interactions under periodic boundaryconditions. A highly optimized implementation of this method is availablein GROMACS, a widely used software for molecular dynamics simulations.In this article, we compare a more recent method from the same family ofmethods, the spectral Ewald (SE) method, to the SPME method in termsof performance and efficiency. We consider serial and parallel implementa-tions of both methods for single and multiple core computations on a desktopmachine as well as the Beskow supercomputer at KTH Royal Institute ofTechnology. The implementation of the SE method has been well optimized,however not yet comparable to the level of the SPME implementation thathas been improved upon for many years. We show that the SE method isvery efficient whenever used to achieve high accuracy and that it already atthis level of optimization can be competitive for low accuracy demands.

Nyckelord [en]
Fast Ewald summation, Fast Fourier transform, Coulomb potentials, SE, SPME, GROMACS
Nationell ämneskategori
Beräkningsmatematik
Forskningsämne
Tillämpad matematik och beräkningsmatematik
Identifikatorer
URN: urn:nbn:se:kth:diva-219771OAI: oai:DiVA.org:kth-219771DiVA, id: diva2:1165198
Forskningsfinansiär
Swedish e‐Science Research CenterSwedish Research Council for Environment, Agricultural Sciences and Spatial Planning, 2011-3178
Anmärkning

QC 20171213

Tillgänglig från: 2017-12-12 Skapad: 2017-12-12 Senast uppdaterad: 2017-12-18Bibliografiskt granskad
Ingår i avhandling
1. Fast methods for electrostatic calculations in molecular dynamics simulations
Öppna denna publikation i ny flik eller fönster >>Fast methods for electrostatic calculations in molecular dynamics simulations
2018 (Engelska)Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
Abstract [en]

This thesis deals with fast and efficient methods for electrostatic calculations with application in molecular dynamics simulations. The electrostatic calculations are often the most expensive part of MD simulations of charged particles. Therefore, fast and efficient algorithms are required to accelerate these calculations. In this thesis, two types of methods have been considered: FFT-based methods and fast multipole methods (FMM).

The major part of this thesis deals with fast N.log(N) and spectrally accurate methods for accelerating the computation of pairwise interactions with arbitrary periodicity. These methods are based on the Ewald decomposition and have been previously introduced for triply and doubly periodic problems under the name of Spectral Ewald (SE) method. We extend the method for problems with singly periodic boundary conditions, in which one of three dimensions is periodic. By introducing an adaptive fast Fourier transform, we reduce the cost of upsampling in the non periodic directions and show that the total cost of computation is comparable with the triply periodic counterpart. Using an FFT-based technique for solving free-space harmonic problems, we are able to unify the treatment of zero and nonzero Fourier modes for the doubly and singly periodic problems. Applying the same technique, we extend the SE method for cases with free-space boundary conditions, i.e. without any periodicity.

This thesis is also concerned with the fast multipole method (FMM) for electrostatic calculations. The FMM is very efficient for parallel processing but it introduces irregularities in the electrostatic potential and force, which can cause an energy drift in MD simulations. In this part of the thesis we introduce a regularized version of the FMM, useful for MD simulations, which approximately conserves energy over a long time period and even for low accuracy requirements. The method introduces a smooth transition over the boundary of boxes in the FMM tree and therefore it removes the discontinuity at the error level inherent in the FMM.

Ort, förlag, år, upplaga, sidor
Stockholm: KTH Royal Institute of Technology, 2018. s. 58
Serie
TRITA-MAT-A ; 2018:02
Nationell ämneskategori
Beräkningsmatematik
Forskningsämne
Tillämpad matematik och beräkningsmatematik
Identifikatorer
urn:nbn:se:kth:diva-219775 (URN)978-91-7729-640-9 (ISBN)
Disputation
2018-01-26, F3, Lindstedtsvägen 26, Stockholm, 10:00 (Engelska)
Opponent
Handledare
Forskningsfinansiär
Swedish e‐Science Research Center
Anmärkning

QC 20171213

Tillgänglig från: 2017-12-13 Skapad: 2017-12-12 Senast uppdaterad: 2017-12-13Bibliografiskt granskad

Open Access i DiVA

Fulltext saknas i DiVA

Övriga länkar

ArXiv

Personposter BETA

Saffar Shamshirgar, DavoodHess, BerkTornberg, Anna-Karin

Sök vidare i DiVA

Av författaren/redaktören
Saffar Shamshirgar, DavoodHess, BerkTornberg, Anna-Karin
Av organisationen
Numerisk analys, NAScience for Life Laboratory, SciLifeLab
Beräkningsmatematik

Sök vidare utanför DiVA

GoogleGoogle Scholar

urn-nbn

Altmetricpoäng

urn-nbn
Totalt: 738 träffar
RefereraExporteraLänk till posten
Permanent länk

Direktlänk
Referera
Referensformat
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Annat format
Fler format
Språk
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Annat språk
Fler språk
Utmatningsformat
  • html
  • text
  • asciidoc
  • rtf