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Accelerating atomic-level protein simulations by flat-histogram techniques.

Jonsson, Sigurdur LU ; Mohanty, Sandipan and Irbäck, Anders LU (2011) In Journal of Chemical Physics 135(12).
Abstract
Flat-histogram techniques provide a powerful approach to the simulation of first-order-like phase transitions and are potentially very useful for protein studies. Here, we test this approach by implicit solvent all-atom Monte Carlo (MC) simulations of peptide aggregation, for a 7-residue fragment (GIIFNEQ) of the Cu/Zn superoxide dismutase 1 protein (SOD1). In simulations with 8 chains, we observe two distinct aggregated/non-aggregated phases. At the midpoint temperature, these phases coexist, separated by a free-energy barrier of height 2.7 k(B)T. We show that this system can be successfully studied by carefully implemented flat-histogram techniques. The frequency of barrier crossing, which is low in conventional canonical simulations,... (More)
Flat-histogram techniques provide a powerful approach to the simulation of first-order-like phase transitions and are potentially very useful for protein studies. Here, we test this approach by implicit solvent all-atom Monte Carlo (MC) simulations of peptide aggregation, for a 7-residue fragment (GIIFNEQ) of the Cu/Zn superoxide dismutase 1 protein (SOD1). In simulations with 8 chains, we observe two distinct aggregated/non-aggregated phases. At the midpoint temperature, these phases coexist, separated by a free-energy barrier of height 2.7 k(B)T. We show that this system can be successfully studied by carefully implemented flat-histogram techniques. The frequency of barrier crossing, which is low in conventional canonical simulations, can be increased by turning to a two-step procedure based on the Wang-Landau and multicanonical algorithms. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Journal of Chemical Physics
volume
135
issue
12
publisher
American Institute of Physics
external identifiers
  • wos:000295619700058
  • pmid:21974561
  • scopus:80053501774
ISSN
0021-9606
DOI
10.1063/1.3643328
language
English
LU publication?
yes
id
95d9206a-b48f-4d8c-a258-22bf0272b9f2 (old id 2200791)
date added to LUP
2011-12-05 08:58:23
date last changed
2017-08-13 03:19:58
@article{95d9206a-b48f-4d8c-a258-22bf0272b9f2,
  abstract     = {Flat-histogram techniques provide a powerful approach to the simulation of first-order-like phase transitions and are potentially very useful for protein studies. Here, we test this approach by implicit solvent all-atom Monte Carlo (MC) simulations of peptide aggregation, for a 7-residue fragment (GIIFNEQ) of the Cu/Zn superoxide dismutase 1 protein (SOD1). In simulations with 8 chains, we observe two distinct aggregated/non-aggregated phases. At the midpoint temperature, these phases coexist, separated by a free-energy barrier of height 2.7 k(B)T. We show that this system can be successfully studied by carefully implemented flat-histogram techniques. The frequency of barrier crossing, which is low in conventional canonical simulations, can be increased by turning to a two-step procedure based on the Wang-Landau and multicanonical algorithms.},
  articleno    = {125102},
  author       = {Jonsson, Sigurdur and Mohanty, Sandipan and Irbäck, Anders},
  issn         = {0021-9606},
  language     = {eng},
  number       = {12},
  publisher    = {American Institute of Physics},
  series       = {Journal of Chemical Physics},
  title        = {Accelerating atomic-level protein simulations by flat-histogram techniques.},
  url          = {http://dx.doi.org/10.1063/1.3643328},
  volume       = {135},
  year         = {2011},
}