Exploring Energy Landscapes: Metrics, Pathways, and Normal-Mode Analysis for Rigid-Body Molecules

Rühle, Victor; Kusumaatmaja, Halim; Chakrabarti, Dwaipayan; Wales, David J.

doi:10.1021/ct400403y

Cited by 21 publications

(35 citation statements)

References 57 publications

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“…47 Significant efficiency gains for global optimisation in biomolecules can be obtained if large moves in configuration space can be proposed without causing groups of bonded atoms to overlap. Here, a group rotation scheme has been successfully applied, [48][49][50] and this approach can be combined with local rigidification of arbitrary sets of atoms, 51 using angleaxis coordinates. 52,53 For two peptides, where benchmarking statistics can still be obtained for less efficient approaches, local rigidification improved the mean first encounter times for the global minima by up to a factor of 4.…”

Section: A Basin-hopping Global Optimisationmentioning

confidence: 99%

“…76 The rate constants for individual minimum-to-minimum transitions can be estimated by any convenient unimolecular rate theory 77 or explicit dynamics. For the simplest harmonic normal mode approximations, the required metric tensor has now been derived for angle-axis coordinates, 48 which enables rates to be obtained for systems involving rigid body molecules and the general local rigidification scheme 49,51 within the discrete path sampling (DPS) framework.…”

Section: Rare Event Dynamicsmentioning

confidence: 99%

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Perspective: Insight into reaction coordinates and dynamics from the potential energy landscape

Wales¹

2015

The Journal of Chemical Physics

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This perspective focuses on conceptual and computational aspects of the potential energy landscape framework. It has two objectives: first to summarise some key developments of the approach and second to illustrate how such techniques can be applied using a specific example that exploits knowledge of pathways. Recent developments in theory and simulation within the landscape framework are first outlined, including methods for structure prediction, analysis of global thermodynamic properties, and treatment of rare event dynamics. We then develop a connection between the kinetic transition network treatment of dynamics and a potential of mean force defined by a reaction coordinate. The effect of projection from the full configuration space to low dimensionality is illustrated for an atomic cluster. In this example, where a relatively successful structural order parameter is available, the principal change in cluster morphology is reproduced, but some details are not faithfully represented. In contrast, a profile based on configurations that correspond to the discrete path defined geometrically retains all the barriers and minima. This comparison provides insight into the physical origins of "friction" effects in low-dimensionality descriptions of dynamics based upon a reaction coordinate.

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Section: A Basin-hopping Global Optimisationmentioning

confidence: 99%

Section: Rare Event Dynamicsmentioning

confidence: 99%

Perspective: Insight into reaction coordinates and dynamics from the potential energy landscape

Wales¹

2015

The Journal of Chemical Physics

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“…65 The metric tensor formulation is consistent with calculations performed on the full atomistic resolution while only making use of the rigid-body variables and the tensor of gyration. A measure for finite distances, which is consistent with the underlying atomistic representation, can also be obtained, and has been used to adapt nudged 66,67 and doubly-nudged 68 elastic band methods in double-ended transition state searches for rigid-body systems.…”

Section: Metric Tensormentioning

confidence: 70%

“…A measure for finite distances, which is consistent with the underlying atomistic representation, can also be obtained, and has been used to adapt nudged 66,67 and doubly-nudged 68 elastic band methods in double-ended transition state searches for rigid-body systems. 65 …”

Section: Metric Tensormentioning

confidence: 99%

Exploring energy landscapes: from molecular to mesoscopic systems

Chakrabarti

Kusumaatmaja

Rühle

et al. 2014

Phys. Chem. Chem. Phys.

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Citation for published item:ghkrrtiD hF nd uusumtmjD rF nd ¤ uhleD F nd lesD hFtF @PHIRA 9ixploring energy lndspes X from moleulr to mesosopi systemsF9D hysil hemistry hemil physisFD IT @IIAF SHIRE SHPSF Further information on publisher's website: Use policyThe full-text may be used and/or reproduced, and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not-for-prot purposes provided that:• a full bibliographic reference is made to the original source • a link is made to the metadata record in DRO • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of the copyright holders.Please consult the full DRO policy for further details. We review a comprehensive computational framework to survey the potential energy landscape for systems composed of rigid or partially rigid molecules. Illustrative case studies relevant to a wide range of molecular clusters and soft and condensed matter systems are discussed.

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“…Rühle et.al. 9 have used an axis-angle presentation to carry out rigid-body rotations for removing the external degrees of freedom in NEB calculations. The method has mainly been applied in calculations of rigid molecules.…”

Section: Introductionmentioning

confidence: 99%

Removing External Degrees of Freedom from Transition-State Search Methods using Quaternions

Melander¹,

Laasonen²,

Jónsson

2015

J. Chem. Theory Comput.

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In finite systems, such as nanoparticles and gas-phase molecules, calculations of minimum energy paths (MEPs) connecting initial and final states of transitions as well as searches for saddle points are complicated by the presence of external degrees of freedom, such as overall translation and rotation. A method based on quaternion algebra for removing the external degrees of freedom is described here and applied in calculations using two commonly used methods: the nudged elastic band (NEB) method for MEPs and the DIMER method for finding the minimum mode in minimum mode following searches of first-order saddle points. With the quaternion approach, fewer images in the NEB are needed to represent MEPs accurately. In both NEB and DIMER calculations of finite systems, the number of iterations required to reach convergence is significantly reduced. The algorithms have been implemented in the Atomic Simulation Environment (ASE) open source software.

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Exploring Energy Landscapes: Metrics, Pathways, and Normal-Mode Analysis for Rigid-Body Molecules

Cited by 21 publications

References 57 publications

Perspective: Insight into reaction coordinates and dynamics from the potential energy landscape

Perspective: Insight into reaction coordinates and dynamics from the potential energy landscape

Exploring energy landscapes: from molecular to mesoscopic systems

Removing External Degrees of Freedom from Transition-State Search Methods using Quaternions

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