An algorithm to find minimum free-energy paths using umbrella integration

Bohner, Matthias U.; Kästner, Johannes

doi:10.1063/1.4736317

Cited by 20 publications

(30 citation statements)

References 45 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Such an approach has already been advocated in conjunction with the UI method. 81 Further, these derivatives would provide biasing forces from a global biasing potential in order to smooth out the free energy landscape for improved sampling such as in metadynamics and adaptive biasing potential methods. 5-8,74-77,82-86 …”

Section: Discussionmentioning

confidence: 99%

A New Maximum Likelihood Approach for Free Energy Profile Construction from Molecular Simulations

Radak

Pabis

et al. 2012

J. Chem. Theory Comput.

150

View full text Add to dashboard Cite

A novel variational method for construction of free energy profiles from molecular simulation data is presented. The variational free energy profile (VFEP) method uses the maximum likelihood principle applied to the global free energy profile based on the entire set of simulation data (e.g from multiple biased simulations) that spans the free energy surface. The new method addresses common obstacles in two major problems usually observed in traditional methods for estimating free energy surfaces: the need for overlap in the re-weighting procedure and the problem of data representation. Test cases demonstrate that VFEP outperforms other methods in terms of the amount and sparsity of the data needed to construct the overall free energy profiles. For typical chemical reactions, only ~5 windows and ~20-35 independent data points per window are sufficient to obtain an overall qualitatively correct free energy profile with sampling errors an order of magnitude smaller than the free energy barrier. The proposed approach thus provides a feasible mechanism to quickly construct the global free energy profile and identify free energy barriers and basins in free energy simulations via a robust, variational procedure that determines an analytic representation of the free energy profile without the requirement of numerically unstable histograms or binning procedures. It can serve as a new framework for biased simulations and is suitable to be used together with other methods to tackle with the free energy estimation problem.

show abstract

Section: Discussionmentioning

confidence: 99%

A New Maximum Likelihood Approach for Free Energy Profile Construction from Molecular Simulations

Radak

Pabis

et al. 2012

J. Chem. Theory Comput.

150

View full text Add to dashboard Cite

show abstract

“…Since this would lead to instabilities in the following optimization, we project out the respective components in accordance with previous work. 22 We orthogonalize the gradient to translation and rotation bỹ…”

Section: A Umbrella Integrationmentioning

confidence: 99%

“…Gray lines show the MFEP and crosses the saddle points obtained in previous work. 22 Red circles mark the images used as estimates for the saddle points. The indices of these images are printed as red numbers.…”

Section: Calculational Detailsmentioning

confidence: 99%

“…3, the projection of the initial guess and the converged paths are shown in a contour map of the potential energy. Our previous results, 22 using the same RCS but with the saddle points found by Newton-Raphson search, are shown in gray for comparison.…”

Section: Examplesmentioning

confidence: 99%

“…Previously, some of us have described a method 22 to find MFEPs by free energy forces obtained from umbrella integration, 23-27 a method to analyze umbrella sampling simulations. There, free energy saddle points were found by a Newton-Raphson search on the free energy surface of the RCS.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Nudged-elastic band used to find reaction coordinates based on the free energy

Bohner

Zeman

Smiatek

et al. 2014

The Journal of Chemical Physics

Self Cite

View full text Add to dashboard Cite

Transition paths characterize chemical reaction mechanisms. In this paper, we present a new method to find mean reaction paths based on the free energy. A nudged elastic band (NEB) is optimized using gradients and Hessians of the free energy, which are obtained from umbrella integration. The transition state can be refined by a Newton-Raphson search starting from the highest point of the NEB path. All optimizations are done using Cartesian coordinates. Independent molecular dynamics (MD) runs are performed at each image used to discretize the path. This makes the method intrinsically parallel. In contrast to other free energy methods, the algorithm does not become more expensive when including more degrees of freedom in the active space. The method is applied to the alanine-dipeptide as a test case and compared to pathways that have been derived from metadynamics and forward flux sampling.

show abstract

Molecular dynamics coupled with a virtual system for effective conformational sampling

et al. 2018

View full text Add to dashboard Cite

An enhanced conformational sampling method is proposed: virtual-system coupled canonical molecular dynamics (VcMD). Although VcMD enhances sampling along a reaction coordinate, this method is free from estimation of a canonical distribution function along the reaction coordinate. This method introduces a virtual system that does not necessarily obey a physical law. To enhance sampling the virtual system couples with a molecular system to be studied. Resultant snapshots produce a canonical ensemble. This method was applied to a system consisting of two short peptides in an explicit solvent. Conventional molecular dynamics simulation, which is ten times longer than VcMD, was performed along with adaptive umbrella sampling. Free-energy landscapes computed from the three simulations mutually converged well. The VcMD provided quicker association/dissociation motions of peptides than the conventional molecular dynamics did. The VcMD method is applicable to various complicated systems because of its methodological simplicity. © 2018 Wiley Periodicals, Inc.

show abstract

An algorithm to find minimum free-energy paths using umbrella integration

Cited by 20 publications

References 45 publications

A New Maximum Likelihood Approach for Free Energy Profile Construction from Molecular Simulations

A New Maximum Likelihood Approach for Free Energy Profile Construction from Molecular Simulations

Nudged-elastic band used to find reaction coordinates based on the free energy

Molecular dynamics coupled with a virtual system for effective conformational sampling

Contact Info

Product

Resources

About