Analysis of the adaptive multilevel splitting method on the isomerization of alanine dipeptide

Lopes, Laura J. S.; Lelièvre, Tony

doi:10.1002/jcc.25778

Cited by 15 publications

(22 citation statements)

References 16 publications

(44 reference statements)

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“…Scripting directives are typically employed to control simulation workflows based on CVs, forming the basis for the implementation of numerical schemes like the string method with swarms of trajectories, 82 or the adaptive multilevel splitting algorithm. 83,84 The primary scripting language of Colvars in NAMD is Tcl. Colvars can be also called from a Python script indirectly through the Tcl interface.…”

Section: Scripting Interfacementioning

confidence: 99%

Scalable molecular dynamics on CPU and GPU architectures with NAMD

Phillips

Hardy

Maia

et al. 2020

The Journal of Chemical Physics

1,965

1,659

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NAMD is a molecular dynamics program designed for high-performance simulations of very large biological objects on central processing unit (CPU)-and graphics processing unit (GPU)-based architectures. NAMD offers scalable performance on petascale parallel supercomputers consisting of hundreds of thousands of cores, as well as on inexpensive commodity clusters commonly found in academic environments. It is written in C++ and leans on Charm++ parallel objects for optimal performance on low-latency architectures. NAMD is a versatile, multipurpose code that gathers state-of-the-art algorithms to carry out simulations in apt thermodynamic ensembles, using the widely popular CHARMM, AMBER, OPLS and GROMOS biomolecular force fields. Here, we review the main features of NAMD that allow both equilibrium and enhanced-sampling molecular dynamics simulations with numerical efficiency. We describe the underlying concepts utilized by NAMD and their implementation, most notably for handling long-range electrostatics, controlling the temperature, pressure and pH, applying external potentials on tailored grids, leveraging massively parallel resources in multiple-copy simulations, as well as hybrid QM/MM descriptions. We detail the variety of options offered by NAMD for enhanced-sampling simulations aimed at determining free-energy differences of either alchemical or geometrical transformations, and outline their applicability to specific problems. Last, we discuss the roadmap for the development of NAMD and our current efforts towards achieving optimal performance on GPUbased architectures, for pushing back the limitations that have prevented biologically realistic billion-atom objects to be fruitfully simulated, and for making large-scale simulations less expensive and easier to set up, run and analyze. NAMD is distributed free of charge with its source code at www.ks.uiuc.edu.

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Section: Scripting Interfacementioning

confidence: 99%

Scalable molecular dynamics on CPU and GPU architectures with NAMD

Phillips

Hardy

Maia

et al. 2020

The Journal of Chemical Physics

1,965

1,659

View full text Add to dashboard Cite

show abstract

“…Several approaches are available. For example, Transition Interface Sampling, 65 Forward flux, 66 weighted ensemble, 67 nonequilibrium umbrella sampling, 68 Adoptive Multilevel Splitting, 69 and more. These approaches are, in principle, exact and enhance the sampling of entire trajectories from reactant to product.…”

Section: Discussionmentioning

confidence: 99%

Modeling molecular kinetics with Milestoning

Elber

Fathizadeh

et al. 2020

WIREs Comput Mol Sci

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Time scales are of paramount importance in biology. Living systems exploit variations in time scales to aim processes in desired directions. The network of biochemical reactions shapes cellular responses and metabolism. Enzymes speed up the rate of reactions and molecular machines carry on cellular tasks. Significant efforts are invested in studying dynamics of biophysical processes and understanding their mechanisms. Experiments provide important clues, but the data can be sparse. Atomically detailed Molecular Dynamics simulations hold the promise of comprehensive pictures of these events. A challenge for simulations is the wide range of time scales in biology, from femtoseconds to hours. Straightforward Molecular Dynamics simulations of kinetics are typically bound by microseconds and unable to probe slower processes. For example, membrane permeation by a small molecule can take hours, slow events in protein folding, seconds, and enzymatic reactions, hundreds of milliseconds. To address these challenges, we introduce the method of Milestoning. Milestoning is a theory and an algorithm to enhance the sampling of kinetic events using computer simulations. Milestoning exploits short trajectories between interfaces of cells in coarse space. Short trajectories are efficient to compute and provide a sequence of approximations that converge to the exact solution. The theory is discussed, and several examples illustrate the use of Milestoning. We consider an enzymatic reaction, peptide permeation through a phospholipid membrane, and the translocation of the lethal factor through the Anthrax channel. The high versatility of Milestoning suggests that it is a useful tool for investigations of complex biomolecular reactions. This article is categorized under: Structure and Mechanism > Computational Biochemistry and Biophysics Molecular and Statistical Mechanics > Molecular Dynamics and Monte‐Carlo Methods Theoretical and Physical Chemistry > Reaction Dynamics and Kinetics

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“…Finally, let us mention another recent application of AMS to isomerization when using the NAMD simulation program [38].…”

Section: Molecular Dynamicsmentioning

confidence: 99%

Adaptive multilevel splitting: Historical perspective and recent results

Cérou

Guyader

Rousset

2019

Chaos: An Interdisciplinary Journal of Nonlinear Science

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About ten years ago, the Adaptive Multilevel Splitting algorithm (AMS) was proposed to analyse rare events in a dynamical setting. This review paper first presents a short historical perpective of the importance splitting approach to simulate and estimate rare events, with a detailed description of several variants. We then give an account of recent theoretical results on these algorithms, including a central limit theorem for Adaptive Multilevel Splitting. Considering the asymptotic variance in the latter, the choice of the importance function, called the reaction coordinate in molecular dynamics, is also discussed. Finally, we briefly mention some worthwhile applications of AMS in various domains.

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Analysis of the adaptive multilevel splitting method on the isomerization of alanine dipeptide

Cited by 15 publications

References 16 publications

Scalable molecular dynamics on CPU and GPU architectures with NAMD

Scalable molecular dynamics on CPU and GPU architectures with NAMD

Modeling molecular kinetics with Milestoning

Adaptive multilevel splitting: Historical perspective and recent results

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