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Free Energy Landscape (FEL) analysis

BD Balint Dudas
DT Daniel Toth
DP David Perahia
AN Arnaud B. Nicot
EB Erika Balog
MM Maria A. Miteva
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FELs of conformations corresponding to the different MD and MDeNM simulations were calculated within the plane defined by the distances d(L1,L2) and d(L1,L3). The most populated state was used as a reference for calculating free energy differences. The free energy difference (ΔGα) of a given state α was determined by considering the probability of the occurrence of the two states P(qα) and Pmax(q) given by the equation:

where kB is the Boltzmann constant, T is the temperature of the simulation, P(qα) is an estimate of the probability density function obtained from the bi-dimensional histogram of the conformations distribution in the plane of d(L1,L2) and d(L1,L3) during the simulation. Pmax(q) is the probability of the most populated state.

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