Modified single sweep method for reconstructing free-energy landscapes

Monteferrante, Michele; Bonella, Sara; Meloni, Simone; Ciccotti, Giovanni

doi:10.1080/08927020903051598

Cited by 15 publications

(18 citation statements)

References 25 publications

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“…In this section we describe three related methods, Temperature Accelerated Molecular Dynamics (TAMD [28]), the associated Temperature Accelerated Monte Carlo (TAMC [4]), and the Single Sweep method (SSM) [29,32], aimed at exploring and computing the free energy of a set of observables, also called collective variables (CVs). We consider the case of CVs that are function of the particles position only, ξ(r) = {ξ i (r)} i=1,M .…”

Section: Methodsmentioning

confidence: 99%

“…it is steeper along some direction and shallower along others, the choice of spherical Gaussians is unjustified and non optimal. The standard SSM can be improved, ISSM [32], by using the more general Gaussian basis set:…”

Section: The Single Sweep Methodsmentioning

confidence: 99%

“…[52] and Refs. [36,39]) and the Single Sweep method (SSM [29,32]) are attempts to solve these problems. They share some ingredients with other methods emerged in the same period, such as the Local Elevation Method [17], and the closely related Conformational Flooding [13] and Metadynamics [23], and the Canonical Adiabatic Free Energy…”

Section: Introductionmentioning

confidence: 99%

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Free energies for rare events: Temperature accelerated MD and MC

Meloni

Ciccotti

2015

Eur. Phys. J. Spec. Top.

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In this article we review a set of methods for exploring the space of a set of collective variables, and to reconstruct the associated Landau free energy in presence of metastabilities: Temperature Accelerated Molecular Dynamics (TAMD), its extension, Temperature Accelerate Monte Carlo (TAMC), and the Single Sweep Method (SSM). TAMD and TAMC can be used for both exploring and reconstructing the Landau free energy landscape. However, SSM is more efficient at accomplishing this last task. We illustrate the use of these methods by presenting their application to the nucleation of a Lennard-Jones crystal from its melt, and the H-vacancy migration in an NaAlH 6 crystal.

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Section: Methodsmentioning

confidence: 99%

Section: The Single Sweep Methodsmentioning

confidence: 99%

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Free energies for rare events: Temperature accelerated MD and MC

Meloni

Ciccotti

2015

Eur. Phys. J. Spec. Top.

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“…For example, in in the past years Sprik and co-workers have largely examined the reliability of DFT-based dynamics to calculate pK a of different molecules: first by using constrained dynamics to build free energy curves along the protonation/deprotonation reaction pathways [14] and more recently by a reversible insertion/removal of protons method [15][16][17] Among methods aimed to overcome barriers and thus compute the free energy curves along a reaction pathway, Vanden-Eijnden [18] developed the single sweep method. Subsequently, Vanden-Eijnden, Ciccotti and their co-workers have shown how this method is suited to be used in different systems and in particular in conjunction with DFT-based dynamics [19][20][21][22][23][24]. For that reason, we have applied this method to the determination of pK a of a weak acid in presence of a highly charged cation to show how and to which extent the metal decreases the pK a of the acid.…”

Section: Introductionmentioning

confidence: 95%

p of silicic acid in presence of La³⁺using single sweep method coupled to DFT-based molecular dynamics

Spezia

Vuilleumier

2013

Molecular Physics

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In this paper we show how it is possible to obtain the pK a of a weak acid (H 4 SiO 4 ) bound to a highly charged cation (La 3 + ) from DFT-based molecular dynamics in a relatively simple, tunable and efficient way. This was done by combining molecular dynamics in bulk water of a La 3 + /H 4 SiO 4 complex with the single sweep method. At this end, we have first performed molecular dynamics runs where a high temperature is assigned on the defined reaction coordinate, here the O-H distance. Then we performed constrained molecular dynamics simulations for selected values of the reaction coordinate along the observed dissociation pathway. The average forces obtained from those constrained simulations are then interpolated to get a final free energy curve. The pK a is obtained by integrating the resulting free energy curve and that of a reference calculation, the autodissociation of water. We then show that the pK a of the silanol groups away from La 3 + is close to the first pK a of silisic acid, while the pK a of the silanol groups interacting with La 3 + is about three units lower.

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“…The calculation can be carried out for a range of σ values in order to find an optimal choice for σ that leads to the lowest mean-squared error. 40 Note that one can also use the modified cost function of Monteferrante et al 42 The functional form of the free energy surface via the linear combination of radial basis functions in Eq. (14) may not provide a transparent picture of the free energy landscape, especially when the dimension is high.…”

Section: B Fes Construction and Representationmentioning

confidence: 99%

Order-parameter-aided temperature-accelerated sampling for the exploration of crystal polymorphism and solid-liquid phase transitions

Chen

et al. 2014

The Journal of Chemical Physics

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The problem of predicting polymorphism in atomic and molecular crystals constitutes a significant challenge both experimentally and theoretically. From the theoretical viewpoint, polymorphism prediction falls into the general class of problems characterized by an underlying rough energy landscape, and consequently, free energy based enhanced sampling approaches can be brought to bear on the problem. In this paper, we build on a scheme previously introduced by two of the authors in which the lengths and angles of the supercell are targeted for enhanced sampling via temperature accelerated adiabatic free energy dynamics [T. Q. Yu and M. E. Tuckerman, Phys. Rev. Lett. 107, 015701 (2011)]. Here, that framework is expanded to include general order parameters that distinguish different crystalline arrangements as target collective variables for enhanced sampling. The resulting free energy surface, being of quite high dimension, is nontrivial to reconstruct, and we discuss one particular strategy for performing the free energy analysis. The method is applied to the study of polymorphism in xenon crystals at high pressure and temperature using the Steinhardt order parameters without and with the supercell included in the set of collective variables. The expected fcc and bcc structures are obtained, and when the supercell parameters are included as collective variables, we also find several new structures, including fcc states with hcp stacking faults. We also apply the new method to the solid-liquid phase transition in copper at 1300 K using the same Steinhardt order parameters. Our method is able to melt and refreeze the system repeatedly, and the free energy profile can be obtained with high efficiency. © 2014 AIP Publishing LLC.

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Modified single sweep method for reconstructing free-energy landscapes

Cited by 15 publications

References 25 publications

Free energies for rare events: Temperature accelerated MD and MC

Free energies for rare events: Temperature accelerated MD and MC

p of silicic acid in presence of La³⁺using single sweep method coupled to DFT-based molecular dynamics

Order-parameter-aided temperature-accelerated sampling for the exploration of crystal polymorphism and solid-liquid phase transitions

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Modified single sweep method for reconstructing free-energy landscapes

Cited by 15 publications

References 25 publications

Free energies for rare events: Temperature accelerated MD and MC

Free energies for rare events: Temperature accelerated MD and MC

p of silicic acid in presence of La3+using single sweep method coupled to DFT-based molecular dynamics

Order-parameter-aided temperature-accelerated sampling for the exploration of crystal polymorphism and solid-liquid phase transitions

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p of silicic acid in presence of La³⁺using single sweep method coupled to DFT-based molecular dynamics