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. Author manuscript; available in PMC: 2022 May 6.
Published in final edited form as: J Phys Chem B. 2021 Apr 27;125(17):4241–4261. doi: 10.1021/acs.jpcb.0c10263

Figure 10.

Figure 10.

Free energy difference of decoupling 3-iodotoluene in the binding site as a function of sampling time. For the EQ approach we show the mean free energy difference across three replicates while for the NEQ approach the free energy estimate was obtained by pooling work values from three replicates and estimating one free energy difference using BAR (Sec. 4.5). The uncertainty estimate in both approaches is the standard deviation across three replicates. Same amount of total simulation time was used for the EQ and the four protocols of the NEQ approach. The different NEQ protocols differ in the length and the number of NEQ transitions. The standard deviation, especially for the EQ approach, was high and the ΔG estimate of the NEQ protocols depended on the transition length, suggesting insufficiencies in sampling.