Optimizing the Calculation of Free Energy Differences in Nonequilibrium Work SQM/MM Switching Simulations
Andreas Schöller, Fiona L. Kearns, H. Lee Woodcock, Stefan Boresch
Abstract
values in good agreement with the reference results. This optimized protocol reduces the computational cost by a factor of 40 compared to earlier work. We also describe two tools/ways of analyzing the raw data to detect sources of poor convergence. Specifically, we find it helpful to analyze the raw data (work values from the NEW switching simulations) in a quasi-time series-like manner. Principal component analysis helps to detect cases where one or more conformational degrees of freedom are different at the low and high level of theory.
Topics & Concepts
Work (physics)Non-equilibrium thermodynamicsConvergence (economics)Degrees of freedom (physics and chemistry)Energy (signal processing)Computer scienceStatistical physicsEnergy storageApplied mathematicsPhysicsMathematicsThermodynamicsQuantum mechanicsPower (physics)EconomicsEconomic growthAdvanced Thermodynamics and Statistical MechanicsSpectroscopy and Quantum Chemical StudiesProtein Structure and Dynamics