I have done FEP simulations and am trying to find a way to report the error related to the values of relative delta G found. I have simulated 20 windows each with an interval of lambda of 0.05. Then used -rerun option from mdrun to perform the same simulation with a lambda value of (lambda+0.05) and (lambda-0.05). G_energy gives out dF as being an average of the exponential value of the difference between the potential energy of my state A and my state B in a logarithmic scale, right? Well I found a lecture given by Berk Hess on Gromacs Workshop in 2007, and there is says that the error estimate could be given by g_analyze -ee. Well, Would this error estimate be over the final value of dF (= -kT ln < exp(-(EB-EA)/kT) >A) over several blocks of my simulation? Being so, I would need to organize the values in a single column so as to look like an xvg input file for g_analyze? Being the final delta delta G a sum of all different lambda intervals, would the error estimate of my final sum be the sum of errors for each interval? Thank you in advance FabrÃcio Bracht
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