Draft Standards for Post-Calculation Health Reports

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Revision as of 14:26, 22 December 2013 by John Chodera (talk | contribs) (Created initial draft of Draft Standards for Post-Calculation Health Reports)
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Purpose

This page contains a discussion regarding a draft standard practice for analyses to be run following an alchemical free energy calculation to provide a "health report" indicating the quality of an alchemical free energy calculations, and identifying some common modes of failure generally known to occur in these types of calculations. The hope is to begin a community discussion on this topic so that multiple implementations of these standard checks will be available for different popular codes.

Division of simulation data into "equilibrated region" and "production analysis region"

Computation of statistical inefficiencies

Verifying acceptable alchemical state overlap

Computation of statistical error

Determining whether the calculation has converged

Detection of infrequent events coupled to the alchemical free energy

Detection of artifacts in the simulation parameters

Cycle closure in relative free energy calculations

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