标题
Perspective: Computer simulations of long time dynamics
作者
关键词
-
出版物
JOURNAL OF CHEMICAL PHYSICS
Volume 144, Issue 6, Pages 060901
出版商
AIP Publishing
发表日期
2016-02-09
DOI
10.1063/1.4940794
参考文献
相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。- Exact milestoning
- (2015) Juan M. Bello-Rivas et al. JOURNAL OF CHEMICAL PHYSICS
- Molecular Simulation Workflows as Parallel Algorithms: The Execution Engine of Copernicus, a Distributed High-Performance Computing Platform
- (2015) Sander Pronk et al. Journal of Chemical Theory and Computation
- Simulations of thermodynamics and kinetics on rough energy landscapes with milestoning
- (2015) Juan M. Bello-Rivas et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- A replica exchange transition interface sampling method with multiple interface sets for investigating networks of rare events
- (2014) David W. H. Swenson et al. JOURNAL OF CHEMICAL PHYSICS
- Modeling kinetics and equilibrium of membranes with fields: Milestoning analysis and implication to permeation
- (2014) Alfredo E. Cardenas et al. JOURNAL OF CHEMICAL PHYSICS
- Optimal Dimensionality Reduction of Multistate Kinetic and Markov-State Models
- (2014) Gerhard Hummer et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Molecular machines
- (2013) Ron Elber et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Milestoning with coarse memory
- (2013) Alexander T. Hawk JOURNAL OF CHEMICAL PHYSICS
- Catch bond-like kinetics of helix cracking: Network analysis by molecular dynamics and Milestoning
- (2013) Steven M. Kreuzer et al. JOURNAL OF CHEMICAL PHYSICS
- Stochastic, resonance-free multiple time-step algorithm for molecular dynamics with very large time steps
- (2013) Ben Leimkuhler et al. MOLECULAR PHYSICS
- Microsecond folding experiments and simulations: a match is made
- (2013) M. B. Prigozhin et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Non-stationary forward flux sampling
- (2012) Nils B. Becker et al. JOURNAL OF CHEMICAL PHYSICS
- Revisiting Molecular Dynamics on a CPU/GPU System: Water Kernel and SHAKE Parallelization
- (2012) A. Peter Ruymgaart et al. Journal of Chemical Theory and Computation
- Unassisted Transport of N-Acetyl-l-tryptophanamide through Membrane: Experiment and Simulation of Kinetics
- (2012) Alfredo E. Cardenas et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Dominant folding pathways of a WW domain
- (2012) S. a Beccara et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- How Conformational Dynamics of DNA Polymerase Select Correct Substrates: Experiments and Simulations
- (2012) Serdal Kirmizialtin et al. STRUCTURE
- Milestoning with transition memory
- (2011) Alexander T. Hawk et al. JOURNAL OF CHEMICAL PHYSICS
- Dominant folding pathways of a peptide chain from ab initio quantum-mechanical simulations
- (2011) Silvio a Beccara et al. JOURNAL OF CHEMICAL PHYSICS
- Efficient multiple time scale molecular dynamics: Using colored noise thermostats to stabilize resonances
- (2011) Joseph A. Morrone et al. JOURNAL OF CHEMICAL PHYSICS
- Free energy of conformational transition paths in biomolecules: The string method and its application to myosin VI
- (2011) Victor Ovchinnikov et al. JOURNAL OF CHEMICAL PHYSICS
- Markov state models based on milestoning
- (2011) Christof Schütte et al. JOURNAL OF CHEMICAL PHYSICS
- MOIL-opt: Energy-Conserving Molecular Dynamics on a GPU/CPU System
- (2011) A. Peter Ruymgaart et al. Journal of Chemical Theory and Computation
- Boxed Molecular Dynamics: Decorrelation Time Scales and the Kinetic Master Equation
- (2011) David R. Glowacki et al. Journal of Chemical Theory and Computation
- Revisiting and Computing Reaction Coordinates with Directional Milestoning
- (2011) Serdal Kirmizialtin et al. JOURNAL OF PHYSICAL CHEMISTRY A
- Dominant reaction pathways in protein folding: A direct validation against molecular dynamics simulations
- (2010) Pietro Faccioli et al. JOURNAL OF CHEMICAL PHYSICS
- The “weighted ensemble” path sampling method is statistically exact for a broad class of stochastic processes and binning procedures
- (2010) Bin W. Zhang et al. JOURNAL OF CHEMICAL PHYSICS
- Milestoning without a Reaction Coordinate
- (2010) Peter Májek et al. Journal of Chemical Theory and Computation
- On the Approximation Quality of Markov State Models
- (2010) Marco Sarich et al. MULTISCALE MODELING & SIMULATION
- Atomically detailed simulation of the recovery stroke in myosin by Milestoning
- (2010) R. Elber et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Nonequilibrium umbrella sampling in spaces of many order parameters
- (2009) Alex Dickson et al. JOURNAL OF CHEMICAL PHYSICS
- Markovian milestoning with Voronoi tessellations
- (2009) Eric Vanden-Eijnden et al. JOURNAL OF CHEMICAL PHYSICS
- Exact rate calculations by trajectory parallelization and tilting
- (2009) Eric Vanden-Eijnden et al. JOURNAL OF CHEMICAL PHYSICS
- ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale
- (2009) M. J. Harvey et al. Journal of Chemical Theory and Computation
- A Gentle Stochastic Thermostat for Molecular Dynamics
- (2009) Ben Leimkuhler et al. JOURNAL OF STATISTICAL PHYSICS
- Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations
- (2009) Frank Noé et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Transition-Path Theory and Path-Finding Algorithms for the Study of Rare Events
- (2008) Weinan E et al. Annual Review of Physical Chemistry
- Rate Constant and Reaction Coordinate of Trp-Cage Folding in Explicit Water
- (2008) Jarek Juraszek et al. BIOPHYSICAL JOURNAL
- Anton, a special-purpose machine for molecular dynamics simulation
- (2008) David E. Shaw et al. COMMUNICATIONS OF THE ACM
- On the assumptions underlying milestoning
- (2008) Eric Vanden-Eijnden et al. JOURNAL OF CHEMICAL PHYSICS
- GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
- (2008) Berk Hess et al. Journal of Chemical Theory and Computation
- General purpose molecular dynamics simulations fully implemented on graphics processing units
- (2008) Joshua A. Anderson et al. JOURNAL OF COMPUTATIONAL PHYSICS
- Coarse Master Equations for Peptide Folding Dynamics†
- (2008) Nicolae-Viorel Buchete et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Harvesting graphics power for MD simulations
- (2008) J.A. van Meel et al. MOLECULAR SIMULATION
Find the ideal target journal for your manuscript
Explore over 38,000 international journals covering a vast array of academic fields.
SearchAdd your recorded webinar
Do you already have a recorded webinar? Grow your audience and get more views by easily listing your recording on Peeref.
Upload Now