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)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/2200791
- author
- Jonsson, Sigurdur
LU
; Mohanty, Sandipan
and Irbäck, Anders
LU
- organization
- publishing date
- 2011
- type
- Contribution to journal
- publication status
- published
- subject
- in
- Journal of Chemical Physics
- volume
- 135
- issue
- 12
- article number
- 125102
- publisher
- American Institute of Physics (AIP)
- 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
- 2016-04-01 10:51:10
- date last changed
- 2025-10-14 09:32:53
@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.}},
author = {{Jonsson, Sigurdur and Mohanty, Sandipan and Irbäck, Anders}},
issn = {{0021-9606}},
language = {{eng}},
number = {{12}},
publisher = {{American Institute of Physics (AIP)}},
series = {{Journal of Chemical Physics}},
title = {{Accelerating atomic-level protein simulations by flat-histogram techniques.}},
url = {{http://dx.doi.org/10.1063/1.3643328}},
doi = {{10.1063/1.3643328}},
volume = {{135}},
year = {{2011}},
}