Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules.

  title={Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules.},
  author={Donald Hamelberg and John T Mongan and J. Andrew Mccammon},
  journal={The Journal of chemical physics},
  volume={120 24},
Many interesting dynamic properties of biological molecules cannot be simulated directly using molecular dynamics because of nanosecond time scale limitations. These systems are trapped in potential energy minima with high free energy barriers for large numbers of computational steps. The dynamic evolution of many molecular systems occurs through a series of rare events as the system moves from one potential energy basin to another. Therefore, we have proposed a robust bias potential function… 

Accelerated molecular dynamics and protein conformational change: a theoretical and practical guide using a membrane embedded model neurotransmitter transporter.

The theory behind accelerated molecular dynamics is reviewed, the approach in the context of modeling protein conformational change is discussed and a detailed, step-by-step explanation of how to perform an accelerated molecular Dynamics simulation using a model neurotransmitter transporter embedded in a lipid cell membrane is provided.

Protecting High Energy Barriers: A New Equation to Regulate Boost Energy in Accelerated Molecular Dynamics Simulations

A new boost equation is presented that prevents oversampling of unfavorable high energy conformational states in molecular dynamics simulations and provides not only better recovery of statistics throughout the simulation but also enhanced sampling of statistically relevant regions in explicit solvent MD simulations.

Enhanced sampling and free energy calculations for protein simulations.

  • Qinghua Liao
  • Chemistry
    Progress in molecular biology and translational science
  • 2020

Advances in enhanced sampling molecular dynamics simulations for biomolecules

In this review, the theoretical basis, practical applications, and recent improvements of both constraint and unconstrained enhanced sampling methods are summarized.

Flooding in GROMACS: Accelerated barrier crossings in molecular dynamics

The flooding technique addresses the major bottleneck of today's atomistic molecular dynamics simulations by inclusion of a flooding potential into the force field and significantly accelerates the escape from the initial energy well without affecting the reaction pathway.

Population Based Reweighting of Scaled Molecular Dynamics

A scaled molecular dynamics method is proposed, which modifies the biomolecular potential energy surface and employs a reweighting scheme based on configurational populations, which is comparable to long conventional molecular dynamics simulations and exhibit better recovery of canonical statistics over methods which employ a potential energy term in re weighting.

Coupling Accelerated Molecular Dynamics Methods with Thermodynamic Integration Simulations

The analysis of the distribution of boost potential along the free energy simulations showed that the new accelerated MD approach samples efficiently both low- and high-energy regions of the potential surface, so the statistics are not compromised in the thermodynamic integration calculations, and the ensemble average can be recovered.

Targeting electrostatic interactions in accelerated molecular dynamics with application to protein partial unfolding.

This work focuses on the study of conformational changes of a low-pH T-domain model in explicit solvent using DISEI-aMD, and shows that the proposed sampling method accelerates conformational rearrangement significantly faster than multiple standard aMD simulations and microsecond long conventional MD simulations.

Achieving Rigorous Accelerated Conformational Sampling in Explicit Solvent.

The results show that RaMD-db is a promisingly fast and efficient sampling method for conformational transitions in explicit solvent, which opens new avenues for understanding biomolecular self-assembly and functional dynamics occurring on long time and length scales.

Variationally Optimized Free-Energy Flooding for Rate Calculation.

A new method to obtain kinetic properties of infrequent events from molecular dynamics simulation using a recently introduced variational approach that effectively accelerates transitions between metastable free energy minima while ensuring bias-free transition states, thus allowing accurate kinetic rates to be obtained.



Recent advances in molecular dynamics simulation towards the realistic representation of biomolecules in solution

Abstract. Coupled advances in empirical force fields and classical molecular dynamics simulation methodologies, combined with the availability of faster computers, has lead to significant progress

A method for accelerating the molecular dynamics simulation of infrequent events

For infrequent-event systems, transition state theory (TST) is a powerful approach for overcoming the time scale limitations of the molecular dynamics (MD) simulation method, provided one knows the

Molecular dynamics simulation of nucleic acids: Successes, limitations, and promise *

An overview of the experiences, some cautionary notes, and recommendations for further study in molecular dynamics simulation of nucleic acids are provided.

Predicting slow structural transitions in macromolecular systems: Conformational flooding.

  • Grubmüller
  • Chemistry
    Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics
  • 1995
Results suggest that the method to predict complex structural (conformational) transitions in irregular or disordered macromolecular systems, such as proteins or glasses, at the atomic level is particularly well suited to study biochemically relevant conformational motions in proteins at a microsecond time scale.

Enhancing systematic motion in molecular dynamics simulation

Molecular dynamics (MD) simulation is an important approach for conformational search. The conformational searching efficiency in MD simulation is greatly limited by the systematic conformational

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

We present the derivation of a new molecular mechanical force field for simulating the structures, conformational energies, and interaction energies of proteins, nucleic acids, and many related

Molecular dynamics simulations of biomolecules

A brief description of the origin and early uses of biomolecular simulations is presented, some recent studies that illustrate the utility of such simulations are outlined and their ever-increasing potential for contributing to biology is discussed.

Molecular dynamics simulation of nucleic acids.

Highlights from the molecular dynamics simulation are the spontaneous observation of A B transitions in duplex DNA in response to the environment, specific ion binding and hydration, and reliable representation of protein-nucleic acid interactions.