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Long-range interactions and parallel scalability in molecular simulations

Patra, Michael LU ; Hyvonen, Marja T.; Falck, Emma; Sabouri-Ghomi, Mohsen; Vattulainen, Ilpo and Karttunen, Mikko (2007) In Computer Physics Communications 176(1). p.14-22
Abstract
Typical biomolecular systems such as cellular membranes, DNA, and protein complexes are highly charged. Thus, efficient and accurate treatment of electrostatic interactions is of great importance in computational modeling of such systems. We have employed the GROMACS simulation package to perform extensive benchmarking of different commonly used electrostatic schemes on a range of computer architectures (Pentium-4, IBM Power 4, and Apple/IBM G5) for single processor and parallel performance up to 8 nodes-we have also tested the scalability on four different networks, namely Infiniband, GigaBit Ethernet, Fast Ethernet, and nearly uniform memory architecture, i.e. communication between CPUs is possible by directly reading from or writing to... (More)
Typical biomolecular systems such as cellular membranes, DNA, and protein complexes are highly charged. Thus, efficient and accurate treatment of electrostatic interactions is of great importance in computational modeling of such systems. We have employed the GROMACS simulation package to perform extensive benchmarking of different commonly used electrostatic schemes on a range of computer architectures (Pentium-4, IBM Power 4, and Apple/IBM G5) for single processor and parallel performance up to 8 nodes-we have also tested the scalability on four different networks, namely Infiniband, GigaBit Ethernet, Fast Ethernet, and nearly uniform memory architecture, i.e. communication between CPUs is possible by directly reading from or writing to other CPUs' local memory. It turns out that the particle-mesh Ewald method (PME) performs surprisingly well and offers competitive performance unless parallel runs on PC hardware with older network infrastructure are needed. Lipid bilayers of sizes 128, 512 and 2048 lipid molecules were used as the test systems representing typical cases encountered in biomolecular simulations. Our results enable an accurate prediction of computational speed on most current computing systems, both for serial and parallel runs. These results should be helpful in, for example, choosing the most suitable configuration for a small departmental computer cluster. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
membranes, GROMACS, lipid, electrostatics, molecular simulations, parallel computing
in
Computer Physics Communications
volume
176
issue
1
pages
14 - 22
publisher
Elsevier
external identifiers
  • wos:000243680100002
  • scopus:33751552165
ISSN
0010-4655
DOI
10.1016/j.cpc.2006.07.017
language
English
LU publication?
yes
id
24f508f2-05d3-47e4-84f5-f6f7e318a1af (old id 677431)
date added to LUP
2007-12-17 10:29:06
date last changed
2017-01-01 07:09:51
@article{24f508f2-05d3-47e4-84f5-f6f7e318a1af,
  abstract     = {Typical biomolecular systems such as cellular membranes, DNA, and protein complexes are highly charged. Thus, efficient and accurate treatment of electrostatic interactions is of great importance in computational modeling of such systems. We have employed the GROMACS simulation package to perform extensive benchmarking of different commonly used electrostatic schemes on a range of computer architectures (Pentium-4, IBM Power 4, and Apple/IBM G5) for single processor and parallel performance up to 8 nodes-we have also tested the scalability on four different networks, namely Infiniband, GigaBit Ethernet, Fast Ethernet, and nearly uniform memory architecture, i.e. communication between CPUs is possible by directly reading from or writing to other CPUs' local memory. It turns out that the particle-mesh Ewald method (PME) performs surprisingly well and offers competitive performance unless parallel runs on PC hardware with older network infrastructure are needed. Lipid bilayers of sizes 128, 512 and 2048 lipid molecules were used as the test systems representing typical cases encountered in biomolecular simulations. Our results enable an accurate prediction of computational speed on most current computing systems, both for serial and parallel runs. These results should be helpful in, for example, choosing the most suitable configuration for a small departmental computer cluster.},
  author       = {Patra, Michael and Hyvonen, Marja T. and Falck, Emma and Sabouri-Ghomi, Mohsen and Vattulainen, Ilpo and Karttunen, Mikko},
  issn         = {0010-4655},
  keyword      = {membranes,GROMACS,lipid,electrostatics,molecular simulations,parallel computing},
  language     = {eng},
  number       = {1},
  pages        = {14--22},
  publisher    = {Elsevier},
  series       = {Computer Physics Communications},
  title        = {Long-range interactions and parallel scalability in molecular simulations},
  url          = {http://dx.doi.org/10.1016/j.cpc.2006.07.017},
  volume       = {176},
  year         = {2007},
}