Leveraging the Information from Markov State Models To Improve the Convergence of Umbrella Sampling Simulations.
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Summary
A method that can quantitatively detect this type of issue and gain further insight into the origin of the slow relaxation timescale is designed and implemented.
- Type
- article
- Published
- 2016-08-03
- Cited by
- 18
- References
- 36
- OpenAlex
- https://openalex.org/W27409349
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:4772384
Keywords
Current (fluid), Higher education, Political science, Psychology, Engineering
References
- The Adaptive Biasing Force Method: Everything You Always Wanted To Know but Were Afraid To Ask
- Extension to the weighted histogram analysis method: combining umbrella sampling with free energy calculations
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- Calculating free energies using average force
- Statistically optimal analysis of samples from multiple equilibrium states.
- Coarse master equations for peptide folding dynamics.
- Potential of Mean Force Calculations: A Multiple-Walker Adaptive Biasing Force Approach
- Replica-exchange molecular dynamics method for protein folding
- Rapid equilibrium sampling initiated from nonequilibrium data
- Exploring the free-energy landscape of a short peptide using an average force.
- Statistically optimal analysis of state-discretized trajectory data from multiple thermodynamic states.
- Separation of a mixture of independent signals using time delayed correlations.
- Achieving ergodic sampling using replica-exchange free-energy calculations
- Beyond microscopic reversibility: Are observable non-equilibrium processes precisely reversible?
- Slow dynamics in protein fluctuations revealed by time-structure based independent component analysis: the case of domain motions.
Cited by
- tICA-Metadynamics: Accelerating Metadynamics by Using Kinetically Selected Collective Variables.
- Systematic Dissociation Pathway Searches Guided by Principal Component Modes
- Evaluating the accuracy of the umbrella sampling plots with different dissociation paths, conformational changes, and structure preparation
- Unfolding dynamics of small peptides biased by constant mechanical forces
- Free energy simulations for protein ligand binding and stability
- Decision functions from supervised machine learning algorithms as collective variables for accelerating molecular simulations
- Folding a viral peptide in different membrane environments: pathway and sampling analyses
- Automated design of collective variables using supervised machine learning.
- Adaptive ensemble simulations of biomolecules
- Potential Mean Force from Umbrella Sampling Simulations: What Can We Learn and What Is Missed?
- Orientational and Folding Thermodynamics via Electric Dipole Moment Restraining.
- Molecular Simulation Study of Protein Conformation Change, Binding Mechanisms, and Allosteric Communication
- Toward a structural identification of metastable molecular conformations.
- OGRe: Optimal Grid Refinement Protocol for Accurate Free Energy Surfaces and Its Application in Proton Hopping in Zeolites and 2D COF Stacking
- Kemeny Constant-Based Optimization of Network Clustering Using Graph Neural Networks
- AutoSIM: Redesigning and automating umbrella sampling for biomolecular conformational transitions.
- Cultural Influences; Expectation; Family Work Relationship; Females; Feminism; Foreign Countries; Higher Education; Japanese; Job Satisfaction; *Life Satisfaction; *Occupational Aspiration; Personal Autonomy; *Quality of Life; Quality of Working Life; Questionnaires; *Self Actualization; *Sociocultural Patterns; Student Characteristics; Student Motivation; Tables (Data); Values; Womens Education; Work Ethic
- Umbrella Sampling Workflows for Fast-Converging PMF Calculations without Artificial WHAM Constraints