Efficient and Unbiased Sampling of Biomolecular Systems in the Canonical Ensemble: A Review of Self‐Guided Langevin Dynamics

Wu, Xiongwu; Damjanović, Ana; Brooks, Bernard R.

doi:10.1002/9781118197714.ch6

Cited by 30 publications

(41 citation statements)

References 86 publications

(214 reference statements)

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“…By incorporating the SGLD partition function into the exchange probability, RXSGLD can maintain a canonical ensemble at its base stage while achieve enhanced conformational searching and sampling. Because SGLD plays a central role in this method, we first briefly introduce the SGLD method [1][2][3]9 and its conformational distribution, followed by a detailed description of the RXSGLD method.…”

Section: Theory and Methodsmentioning

confidence: 99%

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Replica exchanging self-guided Langevin dynamics for efficient and accurate conformational sampling

Hodošček

Brooks

2012

The Journal of Chemical Physics

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This work presents a replica exchanging self-guided Langevin dynamics (RXSGLD) simulation method for efficient conformational searching and sampling. Unlike temperature-based replica exchanging simulations, which use high temperatures to accelerate conformational motion, this method uses self-guided Langevin dynamics (SGLD) to enhance conformational searching without the need to elevate temperatures. A RXSGLD simulation includes a series of SGLD simulations, with simulation conditions differing in the guiding effect and/or temperature. These simulation conditions are called stages and the base stage is one with no guiding effect. Replicas of a simulation system are simulated at the stages and are exchanged according to the replica exchanging probability derived from the SGLD partition function. Because SGLD causes less perturbation on conformational distribution than high temperatures, exchanges between SGLD stages have much higher probabilities than those between different temperatures. Therefore, RXSGLD simulations have higher conformational searching ability than temperature based replica exchange simulations. Through three example systems, we demonstrate that RXSGLD can generate target canonical ensemble distribution at the base stage and achieve accelerated conformational searching. Especially for large systems, RXSGLD has remarkable advantages in terms of replica exchange efficiency, conformational searching ability, and system size extensiveness.

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Section: Theory and Methodsmentioning

confidence: 99%

“…The box size was 30 × 30 × 30 Å. 3 A collision frequency of 1/ps was used to maintain the temperature. We used the CHARMM 22 force field 80 to calculate energies and used the 3D IPS method with a local region radius of 10 Å for electrostatic and Lennard-Jones energy calculation.…”

Section: The β-Hairpin Folding Peptide In Aqueous Solutionsmentioning

confidence: 99%

Replica exchanging self-guided Langevin dynamics for efficient and accurate conformational sampling

Hodošček

Brooks

2012

The Journal of Chemical Physics

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“…1 One dimensional free energy profiles are routinely employed to study various molecular systems with respect to a certain variable/coordinate and many enhanced sampling methods for accurately accomplishing this task have been developed in the past decades. 2 Some of the most widespread include multistage/stratified sampling, 3 statically 4–6 and adaptively 7–9 biased sampling, self-guided dynamics, 10 constrained dynamics, 11,12 as well as multicanonical 13,14 and replica exchange 15 algorithms. In addition, a number of simulation protocols based on non-equilibrium sampling 16–19 have also been recently proposed as well as hybrid algorithms.…”

Section: Introductionmentioning

confidence: 99%

Roadmaps through Free Energy Landscapes Calculated Using the Multidimensional vFEP Approach

Radak

Huang

et al. 2013

J. Chem. Theory Comput.

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The variational free energy profile (vFEP) method is extended to two dimensions and tested with molecular simulation applications. The proposed 2D-vFEP approach effectively addresses the two major obstacles to constructing free energy profiles from simulation data using traditional methods: the need for overlap in the re-weighting procedure and the problem of data representation. This is especially evident as these problems are shown to be more severe in two dimensions. The vFEP method is demonstrated to be highly robust and able to provide stable, analytic free energy profiles with only a paucity of sampled data. The analytic profiles can be analyzed with conventional search methods to easily identify stationary points (e.g. minima and first-order saddle points) as well as the pathways that connect these points. These “roadmaps” through the free energy surface are useful not only as a post-processing tool to characterize mechanisms, but can also serve as a basis from which to direct more focused “on-the-fly” sampling or adaptive force biasing. Test cases demonstrate that 2D-vFEP outperforms other methods in terms of the amount and sparsity of the data needed to construct stable, converged analytic free energy profiles. In a classic test case, the two dimensional free energy profile of the backbone torsion angles of alanine dipeptide, 2D-vFEP needs less than 1% of the original data set to reach a sampling accuracy of 0.5 kcal/mol in free energy shifts between windows. A new software tool for performing one and two dimensional vFEP calculations is herein described and made publicly available.

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“…Up to date a list of SGLD variants has been developed using different formula of the guiding force (see Ref. [78] for details). Particularly, SGMD calculates the guiding force with nonbonded interactions as described above [49, 50], SGLD uses momenta[51] and is also referred to as SGLDp, and SGLDfp uses both forces and momenta[79].…”

Section: Unconstrained Enhanced Sampling Methodsmentioning

confidence: 99%

Unconstrained enhanced sampling for free energy calculations of biomolecules: a review

Miao

McCammon

2016

Molecular Simulation

150

128

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Free energy calculations are central to understanding the structure, dynamics and function of biomolecules. Yet insufficient sampling of biomolecular configurations is often regarded as one of the main sources of error. Many enhanced sampling techniques have been developed to address this issue. Notably, enhanced sampling methods based on biasing collective variables (CVs), including the widely used umbrella sampling, adaptive biasing force and metadynamics, have been discussed in a recent excellent review (Abrams and Bussi, Entropy, 2014). Here, we aim to review enhanced sampling methods that do not require predefined system-dependent CVs for biomolecular simulations and as such do not suffer from the hidden energy barrier problem as encountered in the CV-biasing methods. These methods include, but are not limited to, replica exchange/parallel tempering, self-guided molecular/Langevin dynamics, essential energy space random walk and accelerated molecular dynamics. While it is overwhelming to describe all details of each method, we provide a summary of the methods along with the applications and offer our perspectives. We conclude with challenges and prospects of the unconstrained enhanced sampling methods for accurate biomolecular free energy calculations.

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Efficient and Unbiased Sampling of Biomolecular Systems in the Canonical Ensemble: A Review of Self‐Guided Langevin Dynamics

Cited by 30 publications

References 86 publications

Replica exchanging self-guided Langevin dynamics for efficient and accurate conformational sampling

Replica exchanging self-guided Langevin dynamics for efficient and accurate conformational sampling

Roadmaps through Free Energy Landscapes Calculated Using the Multidimensional vFEP Approach

Unconstrained enhanced sampling for free energy calculations of biomolecules: a review

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