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Cited by 221Advanced Physical and Chemical Molecular InteractionsAdvanced Chemical Physics StudiesProtein Structure and Dynamics

Efficient and Direct Generation of Multidimensional Free Energy Surfaces via Adiabatic Dynamics without Coordinate Transformations

Abrams, Jerry B., Tuckerman, Mark E.·2008·The Journal of Physical Chemistry B
DOI 10.1021/jp805039u
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Abstract

Adiabatic free energy dynamics (AFED) was introduced by Rosso et al. [J. Chem. Phys. 2002, 116, 4389] for computing free energy profiles quickly and accurately using a dynamical adiabatic separation between a set of collective variables or reaction coordinates and the remaining degrees of freedom of a system. This approach has been shown to lead to a significant gain in efficiency versus traditional methods such as umbrella sampling, thermodynamic integration, and free energy perturbation for generating one-dimensional free energy profiles. More importantly, AFED is able to generate multidimensional free energy surfaces efficiently via full sweeps of the surface that rapidly map out the locations of the free energy minima. The most significant drawback to the AFED approach is the need to transform the coordinates into a generalized coordinate system that explicitly contains the collective variables of interest. Recently, Maragliano and Vanden-Eijnden built upon the AFED approach by introducing a set of extended phase-space variables, to which the adiabatic decoupling and high temperature are applied [Chem. Phys. Lett. 2006, 426, 168]. In this scheme, which the authors termed "temperature accelerated molecular dynamics" or TAMD, the need for explicit coordinate transformations is circumvented. The ability of AFED and TAMD to generate free energy surfaces efficiently depends on the thermostatting mechanism employed, since both approaches are inherently nonequilibrium due to the adiabatic decoupling. Indeed, Maragliano and Vanden-Eijnden did not report any direct generation of free energy surfaces within the overdamped Langevin dynamics employed by these authors. Here, we show that by formulating TAMD in a manner that is closer to the original AFED approach, including the generalized Gaussian moment thermostat (GGMT) and multiple time-scale integration, multidimensional free energy surfaces for complex systems can be generated directly from the probability distribution function of the extended phase-space variables. The new TAMD formulation, which we term driven AFED or d-AFED, is applied to compare the conformational preferences of small peptides both in gas phase and in solution for three force fields. The results show that d-AFED/TAMD accurately and efficiently generates free energy surfaces in two collective variables useful for characterizing the conformations, namely, the radius of gyration, R(G), and number of hydrogen bonds, N(H).

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  • In order to observe a rare (activated) event without developing dedicated hardware, one needs to selectively increase the speed at which the pathways related to the transition are traversed, to modify the probability distribution that is sampled during the simulation so that configurations close to the transition state occur more often, or to generate adaptively ensembles of trajectories that覆盖the

    “In order to observe a rare (activated) event without developing dedicated hardware 1 one needs to selectively increase the speed at which the pathways related to the transition are traversed 51,87,88 , to modify the probability distribution that is sampled during the simulation so that configurations that are close to the transition state occur more often 15,89 , or to generate adaptively ens”

    From Unsupervised machine learning in atomistic simulations, between predictions and understanding (2019) · cites this paper as [88]

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Authors
Abrams, J. B., & Tuckerman, M. E.
Affiliations
  • Department of Chemistry, New York University, New York, New York 10003
  • Courant Institute of Mathematical Sciences (US)
Corresponding author
Tuckerman, Mark E.
ORCID
Tuckerman, Mark E.
Venue
The Journal of Physical Chemistry B
Publisher
American Chemical Society (ACS)
Published
2008-11-12
Volume
112
Issue
49
Pages
15742-15757
ISSN
  • 1520-5207 (ISSN-L)
  • 1520-6106
DOI
10.1021/jp805039u
OpenAlex
W2052194343
Cited by
221
References
68
Citations by year
2026: 7 · 2025: 8 · 2024: 15 · 2023: 36 · 2022: 16 · 2021: 15 · 2020: 10 · 2019: 9 · 2018: 24 · 2017: 16 · 2016: 11 · 2015: 7 · 2014: 11 · 2013: 10 · 2012: 8
FWCI
3.68
Type
journal article
Language
en
Open access
closed
Locations
  • The Journal of Physical Chemistry B (publishedVersion)
  • PubMed (publishedVersion)
Topics
  • Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
  • Physical Sciences › Physics and Astronomy › Atomic and Molecular Physics, and Optics › Advanced Chemical Physics Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Keywords
radius of gyration, non-equilibrium molecular dynamics, collective variables

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