Transcription of Methods for calculating Potentials of Mean Force
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Methods for calculating Potentials of Mean Force
School of PhysicsGeorgia Institute of TechnologyUniversity of Illinois at Urbana-ChampaignBeckman Institute for Advanced Science and TechnologyTheoretical and Computational Biophysics GroupMethods for calculatingPotentials of Mean ForceAnthony HazelJames C. GumbartSept. 2017A current version of this tutorial is available list for additional Required programs.. Getting started.. 52 Exploring the pathway with Steered Setting up and running the SMD simulation .. Analysis of the SMD simulation .. 93 Determining the PMF with Adaptive Biasing Setting up and running the ABF simulation .
erate the process of interest in a simulation have been developed. One example is steered molecular dynamics (SMD) (1, 2), a method in which forces are ap-plied to part of the system, e.g., the substrate, to drive it along a prede ned direction. Commonly implemented using a constant force or a constant veloc-
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