Efficient Exploration of Reactive Potential Energy Surfaces Using Car-Parrinello Molecular Dynamics

Iannuzzi, Marcella; Laio, Alessandro; Parrinello, Michele

doi:10.1103/physrevlett.90.238302

Cited by 771 publications

(964 citation statements)

References 29 publications

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“…Some variants have been introduced, with the intent of improving the accuracy or the efficiency of the method. 33,34 In ORAC we have used Lucy's functions 35 as a very efficient alternative to the use of Gaussians. A Lucy's function is defined as *…”

Section: Implementation In Oracmentioning

confidence: 99%

ORAC: A molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level

et al. 2009

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Abstract:We present the new release of the ORAC engine (Procacci et al., Comput Chem 1997, 18, 1834, a FORTRAN suite to simulate complex biosystems at the atomistic level. The previous release of the ORAC code included multiple time steps integration, smooth particle mesh Ewald method, constant pressure and constant temperature simulations. The present release has been supplemented with the most advanced techniques for enhanced sampling in atomistic systems including replica exchange with solute tempering, metadynamics and steered molecular dynamics. All these computational technologies have been implemented for parallel architectures using the standard MPI communication protocol. ORAC is an open-source program distributed free of charge under the GNU general public license (GPL) at

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Section: Implementation In Oracmentioning

confidence: 99%

ORAC: A molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level

et al. 2009

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“…Several approaches have recently been developed to increase the simulation efficiency. [10][11][12][13][14][15][16][17][18] However, the majority of these methods achieve this by disturbing the physically correct dynamics of the system. Transition path sampling (TPS), 19 on the other hand, samples unbiased molecular dynamics trajectories via a Monte Carlo (MC) procedure.…”

Section: Introductionmentioning

confidence: 99%

PyRETIS: A well‐done, medium‐sized python library for rare events

2017

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Transition Path Sampling techniques are becoming common approaches in the study of rare events at the molecular scale. More efficient methods, such as transition interface sampling (TIS) and replica exchange transition interface sampling (RETIS), allow the investigation of rare events, e.g. chemical reactions and structural/morphological transitions, in a reasonable computational time. Here, we present PyRETIS, a Python library for performing TIS and RETIS simulations. PyRETIS directs molecular dynamics (MD) simulations in order to sample rare events with unbiased dynamics. PyRETIS is designed to be easily interfaced with any molecular simulation package and in the present release, it has been interfaced with GROMACS and CP2K, for classical and ab initio MD simulations, respectively.

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“…The idea is to extend the phase-space so as to include the reaction coordinates as additional dynamical variables. [ILP03] works in the Hamiltonian context, but we will consider the case of overdamped dynamics which is better suited for analysis. Metadynamics amounts to considering the thermally perturbed gradient flow on the extended energy…”

Section: Metadynamicsmentioning

confidence: 99%

“…[ILP03] works in the Hamiltonian context and use (64), but we will stick to (60). The idea in [ILP03] is to use (64) at large µ and large M Q (with µ/M Q small) to compute the free energy associated withρ(q). Here we show that this free energy can also be computed from (60) at large µ and large δ with µ/δ small.…”

Section: Metadynamicsmentioning

confidence: 99%

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Metastability, conformation dynamics, and transition pathways in complex systems

Weinan

Vanden‐Eijnden

2004

Multiscale Modelling and Simulation

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Summary. We present a systematic introduction to the basic concepts and techniques for determining transition pathways and transition rates in systems with multiple metastable states. After discussing the classical transition state theory and its limitations, we derive a new set of equations for the optimal dividing surfaces. We then discuss transition path sampling, which is the most general technique currently available for determining transition regions and rates. This is followed by a discussion on minimal energy path for systems with smooth energy landscapes. For systems with rough energy landscapes, our presentation is centered around the notion of reaction coordinates. We discuss the two related notions of free energies associated with a reaction coordinate, and show that at least in the high friction limit, there does exist an optimal reaction coordinate that gives asymptotically the correct prediction for the transition rates. Variational principles associated with the optimal reaction coordinates are exploited under the assumption that the transition paths are restricted to tubes, and this provides a theoretical justification for the finite temperature string method. Blue moon sampling techniques, metadynamics and a new form of accelerated dynamics are also discussed.

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Efficient Exploration of Reactive Potential Energy Surfaces Using Car-Parrinello Molecular Dynamics

Cited by 771 publications

References 29 publications

ORAC: A molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level

ORAC: A molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level

PyRETIS: A well‐done, medium‐sized python library for rare events

Metastability, conformation dynamics, and transition pathways in complex systems

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