TY - JOUR
T1 - Simulating Met-Enkephalin With Population Annealing Molecular Dynamics
AU - Christiansen, Henrik
AU - Weigel, Martin
AU - Janke, Wolfhard
N1 - (CC BY) Content from this work may be used under the terms of the Creative Commons Attribution 3.0 licence. Any further distribution of this work must maintain attribution to the author(s) and the title of the work, journal citation and DOI. Published under licence by IOP Publishing Ltd
PY - 2022/3/1
Y1 - 2022/3/1
N2 - Met-enkephalin, one of the smallest opiate peptides and an important neuro-transmitter, is a widely used benchmarking problem in the field of molecular simulation. Through its range of possible low-temperature conformations separated by free-energy barriers it was previously found to be hard to thermalize using straight canonical molecular dynamics simulations. Here, we demonstrate how one can use the recently proposed population annealing molecular dynamics scheme to overcome these difficulties. We show how the use of multi-histogram reweighting allows one to accurately estimate the density of states of the system and hence derive estimates such as the potential energy as quasi continuous functions of temperature. We further investigate the free-energy surface as a function of end-to-end distance and radius-of-gyration and observe two distinct basins of attraction.
AB - Met-enkephalin, one of the smallest opiate peptides and an important neuro-transmitter, is a widely used benchmarking problem in the field of molecular simulation. Through its range of possible low-temperature conformations separated by free-energy barriers it was previously found to be hard to thermalize using straight canonical molecular dynamics simulations. Here, we demonstrate how one can use the recently proposed population annealing molecular dynamics scheme to overcome these difficulties. We show how the use of multi-histogram reweighting allows one to accurately estimate the density of states of the system and hence derive estimates such as the potential energy as quasi continuous functions of temperature. We further investigate the free-energy surface as a function of end-to-end distance and radius-of-gyration and observe two distinct basins of attraction.
UR - http://www.scopus.com/inward/record.url?scp=85128981828&partnerID=8YFLogxK
U2 - 10.1088/1742-6596/2241/1/012006
DO - 10.1088/1742-6596/2241/1/012006
M3 - Conference article
VL - 2241
JO - Journal of Physics: Conference Series
JF - Journal of Physics: Conference Series
SN - 1742-6588
IS - 1
M1 - 012006
T2 - 33rd Annual CSP Workshop: Recent Developments in Computer Simulation Studies in Condensed Matter Physics
Y2 - 17 February 2021 through 21 March 2021
ER -