Exploring high dimensional free energy landscapes: Temperature accelerated sliced sampling

Awasthi, Shalini; Nair, Nisanth N.

doi:10.1063/1.4977704

Cited by 53 publications

(87 citation statements)

References 51 publications

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“…We could successfully simulate the proton exchange reaction using the Temperature Accelerated Sliced Sampling (TASS) method (Awasthi and Nair, 2017 ). This method allowed us to explore a high–dimensional free energy landscape composed of five collective variables (CVs).…”

Section: Resultsmentioning

confidence: 99%

Interfacing the Core-Shell or the Drude Polarizable Force Field With Car–Parrinello Molecular Dynamics for QM/MM Simulations

Sahoo

Nair

2018

Front. Chem.

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We report a quantum mechanics/polarizable–molecular mechanics (QM/p–MM) potential based molecular dynamics (MD) technique where the core–shell (or the Drude) type polarizable MM force field is interfaced with the plane-wave density functional theory based QM force field which allows Car–Parrinello MD for the QM subsystem. In the QM/p-MM Lagrangian proposed here, the shell (or the Drude) MM variables are treated as extended degrees of freedom along with the Kohn–Sham (KS) orbitals describing the QM wavefunction. The shell and the KS orbital degrees of freedom are then adiabatically decoupled from the nuclear degrees of freedom. In this respect, we also present here the Nosé–Hoover Chain thermostat implementation for the dynamical subsystems. Our approach is then used to investigate the effect of MM polarization on the QM/MM results. Especially, the consequence of MM polarization on reaction free energy barriers, defect formation energy, and structural and dynamical properties are investigated. A low point charge polarizable potential (p–MZHB) for pure siliceous systems is also reported here.

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Section: Resultsmentioning

confidence: 99%

Interfacing the Core-Shell or the Drude Polarizable Force Field With Car–Parrinello Molecular Dynamics for QM/MM Simulations

Sahoo

Nair

2018

Front. Chem.

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“…To overcome this problem, Awasthi et al combined US with metadynamics (which we termed as “well‐sliced metadynamics”), where the CV along which a flat unbound free energy surface is expected is sampled by US in a controlled manner, while the orthogonal coordinates are sampled by well‐tempered metadynamics . Well‐sliced metadynamics approach was then extended to accommodate large number of CVs, by combining it with TAMD/d‐AFED approach . This method is called temperature‐accelerated sliced sampling (TASS).…”

Section: Temperature‐accelerated Sliced Samplingmentioning

confidence: 99%

“…In this way, TASS samples a high‐dimensional slice of the free energy surface along the US coordinate. Biased probability distribution obtained from each slice h ,

{\overset{false˜}{P}}_{h} ((), s)

, is then reweighted, as in Equation , and then combined using the WHAM method; see References 58 and 146 for more details. As in the TAMD/d‐AFED method, free energy can be obtained using Equation .…”

Section: Temperature‐accelerated Sliced Samplingmentioning

confidence: 99%

“…Awasthi and Nair have showed the applicability of the method for computing free energy surfaces of chemical reactions in AIMD and hybrid QM/MM MD simulations . Free energy surface of alanine tripeptide was also mapped using four CVs, and free energies were showing good convergence within 10 ns per umbrella window (and 31 umbrella windows were used) . Awasthi et al used TASS to study deacylation and reverse acylation reactions of aztreonam drug catalyzed by class‐C β lactamase enzyme.…”

Section: Temperature‐accelerated Sliced Samplingmentioning

confidence: 99%

“…It was observed that the free energy barrier converges within 9 ps (per umbrella window) . The converged free energy surface was computed using the reweighting procedure explained in Reference 146 and then projected to CV1 and CV2 as shown in Figure .…”

Section: Temperature‐accelerated Sliced Samplingmentioning

confidence: 99%

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Exploring high‐dimensional free energy landscapes of chemical reactions

Awasthi

Nair

2018

WIREs Comput Mol Sci

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Molecular dynamics (MD) techniques are widely used in computing free energy changes for conformational transitions and chemical reactions, mainly in condensed matter systems. Most of the MD-based approaches employ biased sampling of a priori selected coarse-grained coordinates or collective variables (CVs) and thereby accelerate otherwise infrequent transitions from one free energy basin to the other. A quick convergence in free energy estimations can be achieved by enhanced sampling of large number of CVs. Conventional enhanced sampling approaches become exponentially slower with increasing dimensionality of the CV space, and thus they turn out to be highly inefficient in sampling high-dimensional free energy landscapes. Here, we focus on some of the novel methods that are designed to overcome this limitation. In particular, we discuss four methods: biasexchange metadynamics, parallel-bias metadynamics, adiabatic free energy dynamics/temperature-accelerated MD, and temperature-accelerated sliced sampling. The basic idea behind these techniques is presented and applications using these techniques are illustrated. Advantages and disadvantages of these techniques are also delineated.adiabatic free energy dynamics, bias exchange metadyanmics, enhanced sampling, free energy calculations, parallel-bias metadynamics, temperatureaccelerated sliced sampling 1 | INTRODUCTION Free energy changes along the reaction coordinate of a chemical reaction manifests the feasibility of the process at a given temperature. Reaction coordinate, χ, on the other hand, can be an intricate function of nuclear coordinates even for a simple elementary reaction. To simplify, χ can be written as a linear combination of several coarse-grained coordinates or collective variables (CVs), S, as,

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Refined metadynamics through canonical sampling using time‐invariant bias potential: A study of polyalcohol dehydration in hot acidic solutions

et al. 2020

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We propose a canonical sampling method to refine metadynamics simulations a posteriori, where the hills obtained from metadynamics are used as a time-invariant bias potential. In this way, the statistical error in the computed reaction barriers is reduced by an efficient sampling of the collective variable space at the free energy level of interest. This simple approach could be useful particularly when two or more free energy barriers are to be compared among chemical reactions in different or competing conditions. The method was then applied to study the acid dependence of polyalcohol dehydration reactions in high-temperature aqueous solutions. It was found that the reaction proceeds consistently via an S N 2 mechanism, whereby the free energy of protonation of the hydroxyl group created as an intermediate is affected significantly by the acidic species. Although demonstration is shown for a specific problem, the computational method suggested herein could be generally used for simulations of complex reactions in the condensed phase.

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Exploring high dimensional free energy landscapes: Temperature accelerated sliced sampling

Cited by 53 publications

References 51 publications

Interfacing the Core-Shell or the Drude Polarizable Force Field With Car–Parrinello Molecular Dynamics for QM/MM Simulations

Interfacing the Core-Shell or the Drude Polarizable Force Field With Car–Parrinello Molecular Dynamics for QM/MM Simulations

Exploring high‐dimensional free energy landscapes of chemical reactions

Refined metadynamics through canonical sampling using time‐invariant bias potential: A study of polyalcohol dehydration in hot acidic solutions

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