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New ways to boost molecular dynamics simulations

Elmar Krieger, Gert Vriend
2015 Journal of Computational Chemistry  
Acknowledgments The simulation algorithms are used for protein refinement tasks in the NewProt protein modeling project ( E.  ...  Krieger is the owner of the company that distributes YASARA, and would like to thank the YASARA users for providing invaluable feedback and financial support, Prof.  ...  We do not claim that the densostat can replace the virial calculation in all the other applications of molecular dynamics simulations, but we found no influence on the dynamics of the simulated system.  ... 
doi:10.1002/jcc.23899 pmid:25824339 fatcat:lzh423rfurd6plytunrqlrwila

Accelerating the Dynamics of Infrequent Events: Combining Hyperdynamics and Parallel Replica Dynamics to Treat Epitaxial Layer Growth

A. F. Voter, T. C. Germann
1998 Materials Research Society Symposium Proceedings  
HY PERDYNAMICS As discussed above, the goal is to develop a method for extending the time available to a molecular dynamics (MD) simulation.  ...  In contrast to a kinetic Monte Carlo approach, hyperdynamics has the character of a regular molecular dynamics simulation.  ... 
doi:10.1557/proc-528-221 fatcat:u3qha26ivvdkrib7oyy4qr7bxa

Long-time atomistic dynamics through a new self-adaptive accelerated molecular dynamics method

N Gao, L Yang, F Gao, R J Kurtz, D West, S Zhang
2017 Journal of Physics: Condensed Matter  
Accelerated molecular dynamics simulation of thin-film growth with the bond-boostmethod Kristen A Fichthorn, Radu A Miron, Yushan Wang et al.  ...  Key in the new development is the use of the total displacement of the system at a given temperature to construct a boost-potential, which is slowly increased to accelerate the dynamics.  ...  in most accelerated molecular dynamics simulations.  ... 
doi:10.1088/1361-648x/aa574b pmid:28059774 fatcat:bp5yubt3czha7i5vuji7kzug24

Coupling Accelerated Molecular Dynamics Methods with Thermodynamic Integration Simulations

César Augusto F. de Oliveira, Donald Hamelberg, J. Andrew McCammon
2008 Journal of Chemical Theory and Computation  
We also introduce a new accelerated Molecular Dynamics (MD) approach in which molecular conformational transitions are accelerated by lowering the energy barriers while the potential surfaces near the  ...  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  ...  In the dual boost approach, the boost factor is given by exp{ [∆V t (r)+∆V T (r)]}. New Accelerated MD Approach.  ... 
doi:10.1021/ct800160q pmid:19461868 pmcid:PMC2646661 fatcat:3zt7gz4rwjgdbpttsls4ygsbdu

Adaptive Accelerated Molecular Dynamics (Ad-AMD) Revealing the Molecular Plasticity of P450cam

Phineus R. L. Markwick, Levi C. T. Pierce, David B. Goodin, J. Andrew McCammon
2011 Journal of Physical Chemistry Letters  
These methods include replica exchange MD, 10 meta-dynamics, 11 and accelerated molecular dynamics (AMD). 12 The principle behind AMD is to add a continuous non-negative bias potential to the actual PES  ...  to dynamic averaging on the micro-to millisecond time scale.  ...  A more efficient extension to the accelerated molecular dynamics approach is Ad-AMD.  ... 
doi:10.1021/jz101462n pmid:21307966 pmcid:PMC3034398 fatcat:eqot3lu3mrh6dpuaojr66s25mi

Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units

Steffen Lindert, Denis Bucher, Peter Eastman, Vijay Pande, J. Andrew McCammon
2013 Journal of Chemical Theory and Computation  
The accelerated molecular dynamics (aMD) method has recently been shown to enhance the sampling of biomolecules in molecular dynamics (MD) simulations, often by several orders of magnitude.  ...  The new AMOEBA-aMD method is publicly available (http://wiki.simtk. org/openmm/VirtualRepository) and promises to be interesting for studying complex systems that can benefit from both the use of a polarizable  ...  ■ INTRODUCTION Molecular dynamics (MD) is one of the most prominent techniques used to study the dynamics and equilibrium properties of biomolecules.  ... 
doi:10.1021/ct400514p pmid:24634618 pmcid:PMC3948463 fatcat:a4ru65cm3zda3fa3o6z2i4nvgu

Extending the Time Scale in Atomistic Simulation of Materials

Arthur F. Voter, Francesco Montalenti, Timothy C. Germann
2002 Annual review of materials research (Print)  
We discuss promising new methods, derived from transition state theory, for accelerating molecular dynamics simulations of these infrequent-event processes.  ...  s Abstract Obtaining a good atomistic description of diffusion dynamics in materials has been a daunting task owing to the time-scale limitations of the molecular dynamics method.  ...  Deposition of each new atom was performed using direct molecular dynamics for 2 ps, while the intervening time (0.3 s on average for this 50 atom/layer simulation cell) was simulated using the TAD method  ... 
doi:10.1146/annurev.matsci.32.112601.141541 fatcat:6nsqb6xuizdqpbf4fdc2v3cyca

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

William Sinko, César Augusto F. de Oliveira, Levi C. T. Pierce, J. Andrew McCammon
2011 Journal of Chemical Theory and Computation  
Recently, our group has employed accelerated molecular dynamics (aMD) to improve the conformational sampling over conventional molecular dynamics techniques.  ...  To address this issue, in this work, we present a new boost equation that prevents oversampling of unfavorable high energy conformational states.  ...  In an effort to extend the time scale of all-atom molecular dynamics simulations of biomolecules, our group recently proposed an enhanced sampling technique called accelerated molecular dynamics (aMD).  ... 
doi:10.1021/ct200615k pmid:22241967 pmcid:PMC3254191 fatcat:bb6plgdj2zgrpop7g33junyvq4

Molecular dynamics-based approaches for enhanced sampling of long-time, large-scale conformational changes in biomolecules

Tamar Schlick
2009 F1000 Biology Reports  
The rugged energy landscape of biomolecules together with shortcomings of traditional molecular dynamics (MD) simulations require specialized methods for capturing large-scale, long-time configurational  ...  changes along with chemical dynamics behavior.  ...  GROningen MAchine for Chemical Simulation; IMD, interactive molecular dynamics; LES, locally enhanced sampling; LIN; Langevin, implicit Eular and normalmode; MC, Monte Carlo; MD, molecular dynamics;  ... 
doi:10.3410/b1-51 pmid:20948633 pmcid:PMC2948272 fatcat:c5dragh2gvhifgx2sh3mhmfrvu

Adaptive-boost molecular dynamics simulation of carbon diffusion in iron

Akio Ishii, Shigenobu Ogata, Hajime Kimizuka, Ju Li
2012 Physical Review B  
We have developed an accelerated molecular dynamics (MD) method to model atomic-scale rare events.  ...  to accelerate the MD simulation.  ...  Molecular dynamics (MD), a conventional atomistic simulation method, provides detailed atomic trajectory r(t) and information regarding the thermodynamics and "fast" dynamics of solids.  ... 
doi:10.1103/physrevb.85.064303 fatcat:axpsyz6j6jhytlmlwo2jvog6ym

Accounting for Receptor Flexibility and Enhanced Sampling Methods in Computer-Aided Drug Design

William Sinko, Steffen Lindert, J. Andrew McCammon
2012 Chemical Biology and Drug Design  
Here, we review a number of techniques that have been proposed to accommodate receptor flexibility in the simulation of small molecules binding to protein receptors.  ...  The understanding and allowance for receptor flexibility are helping to make computer simulations of ligand protein binding more accurate.  ...  Accelerated Molecular Dynamics Accelerated molecular dynamics (60) , an extension of hyperdynamics (61) , is a simulation method that does not require the selection of a reaction coordinate or CVs and  ... 
doi:10.1111/cbdd.12051 pmid:23253130 pmcid:PMC3540989 fatcat:tso4kv2zqrfmndvfkekcw3f24a

Chapter 4 Accelerated Molecular Dynamics Methods: Introduction and Recent Developments [chapter]

Danny Perez, Blas P. Uberuaga, Yunsic Shim, Jacques G. Amar, Arthur F. Voter
2009 Annual Reports in Computational Chemistry  
In this paper, we present an introduction to accelerated molecular dynamics, a class of methods aimed at extending the timescale range of molecular dynamics, sometimes up to seconds or more.  ...  However, due to computational cost, MD simulations can only be used to directly simulate dynamical processes over limited timescales (e.g., nanoseconds or at most a few microseconds), even though the simulation  ...  We have developed three methods in this accelerated molecular dynamics (AMD) class, in each case appealing to TST, either implicitly or explicitly, to design the modified dynamics.  ... 
doi:10.1016/s1574-1400(09)00504-0 fatcat:nzyi36s3xje3hd55xycsheec3a

On the mechanisms of ionic conductivity in BaLiF3: a molecular dynamics study

Dirk Zahn, Sven Herrmann, Paul Heitjans
2011 Physical Chemistry, Chemical Physics - PCCP  
Direct molecular dynamics simulations of (quasi) single crystalline super cell models hint at the preferred mobility mechanism which is based on fluoride interstitial (and to a smaller extent F À vacancy  ...  The mechanisms of ionic conductivity in BaLiF 3 are investigated using molecular simulations.  ...  Mechanisms of charge carrier migration While high-temperature molecular dynamics simulations are required to boost the formation of Frenkel defects, the subsequent migration of F À interstitials and vacancies  ... 
doi:10.1039/c1cp22495f pmid:22052020 fatcat:yytcyudl7zbrficosdfkltmobu

Hypermolecular dynamics simulations of monovacancy diffusion

X.M. Duan, D.Y. Sun, X.G. Gong
2001 Computational materials science  
The validity of hypermolecular dynamics (hyper-MD) to vacancy diusion is explored.  ...  We have obtained the diffusion constants of a monovacancy up to temperatures as low as 300 K for Al bulk and 160 K for the Al(1 0 0) surface with very large boost factors.  ...  Recently, Voter provided a method to accelerate molecular dynamics, i.e., hyper-MD [15, 16] , which opened a window to the simulation of atomic dynamics for a microsecond or longer.  ... 
doi:10.1016/s0927-0256(00)00172-5 fatcat:52fsqj2uvvg7xiv4f7vxm6juwi

Boosted Hybrid Method for Solving Chemical Reaction Systems with Multiple Scales in Time and Population Size

Yucheng Hu, Assyr Abdulle, Tiejun Li
2012 Communications in Computational Physics  
AbstractA new algorithm, called boosted hybrid method, is proposed for the simulation of chemical reaction systems with scale-separation in time and disparity in species population.  ...  For such stiff systems, the algorithm can automatically identify scale-separation in time and slow down the fast reactions while maintaining a good approximation to the original effective dynamics.  ...  The authors also thank the referees for their constructive comments and suggestions to improve the current paper.  ... 
doi:10.4208/cicp.190411.301111a fatcat:rqiux7endnedtbovmmrthidemm
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