[gmx-users] Tutorial for calculating diffusion from umbrella sampling

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Tue Dec 5 14:27:32 CET 2017


            Dear Experts,Is there any tutorial available online for understanding procedure to calculate diffusion coefficient from umbrella sampled force and position trajectory data. The formula for diffusion is given as D(<z>)=variance(z)/tau. Numerator is variance of z (or reaction coordinate) and denominator is the characteristic time. Reference for the equation is “Gerhard Hummer 2005 New J. Phys. 7 34”As a novice in MD, it’s very difficult to understand the Gerhard paper. Dow anybody have any idea about how to implement this equation.ThanksYogiSent using Zoho Mail


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