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How to run these simulations using Amber. vs. Cazuela sampling? Solved iteratively using e.g. the WHAM program by Alan Grossfield. Constructing the PMF. This tutorial shows how to use the AMBER programs to do umbrella $WHAM/wham P -180.0 180.0 90 0.0001 300.0 0 metadatafile butane.pmf wham.log. 24 Feb 2012 tutorial for running replica exchange molecular dynamics in AMBER then The output of the WHAM calculation (in this case of REMD) is the I have written a fast, memory efficient implementation of the Weighted Histogram Analysis Method (WHAM). I've compiled and tested on a number of platforms Tutorial to run AMBER umbrella COM restraint code and derive free energy of This is due to differences in how restraints are defined in AMBER vs WHAM. Tutorials for Modular Reweighting software. Tutorial 1) Replica exchange molecular dynamics in AMBER with WHAM postprocessing and bootstrap errorThe exact workings of WHAM are beyond the scope of this tutorial whose main aim is to show how to perform umbrella sampling in AMBER rather than to Umbrella Sampling using Amber - Section 2. AMBER Advanced Tutorial 17 . It is not required that the potential actually be harmonic, however, the WHAM (Note: These tutorials are meant to provide illustrative examples of how to use the Method (WHAM) of Alan Grossfield to generate potentials of mean force. ambermd.org/tutorials/advanced/tutorial10/ . The Weighted Histogram Analysis Method (WHAM) [42] was used to unbias the umbrella-sampling results