Comparing geometric and kinetic cluster algorithms for molecular simulation data

2010 ◽  
Vol 132 (7) ◽  
pp. 074110 ◽  
Author(s):  
Bettina Keller ◽  
Xavier Daura ◽  
Wilfred F. van Gunsteren
Keyword(s):  
Molecular Simulation ◽  
Simulation Data ◽  
Cluster Algorithms

Thermodynamic correlation of molecular simulation data

2015 ◽  
Vol 113 (9-10) ◽  
pp. 910-931 ◽  
Author(s):  
Rolf Lustig ◽  
Gabor Rutkai ◽  
Jadran Vrabec
Keyword(s):  
Molecular Simulation ◽  
Simulation Data ◽  
Thermodynamic Correlation

scholarly journals A simple method for automated equilibration detection in molecular simulations

2015 ◽  
Author(s):  
John D Chodera
Keyword(s):  
Data Analysis ◽  
Molecular Simulation ◽  
Molecular Simulations ◽  
Equilibration Time ◽  
Simulation Data ◽  
Traditional Practice ◽  
Initial Portion ◽  
Simple Method ◽  
Initial Transient ◽  
Reference Implementation

Molecular simulations intended to compute equilibrium properties are often initiated from configurations that are highly atypical of equilibrium samples, a practice which can generate a distinct initial transient in mechanical observables computed from the simulation trajectory. Traditional practice in simulation data analysis recommends this initial portion be discarded to equilibration, but no simple, general, and automated procedure for this process exists. Here, we suggest a conceptually simple automated procedure that does not make strict assumptions about the distribution of the observable of interest, in which the equilibration time is chosen to maximize the number of effectively uncorrelated samples in the production timespan used to compute equilibrium averages. We present a simple Python reference implementation of this procedure, and demonstrate its utility on typical molecular simulation data.

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