Hi, I am trying to calculate free energy of a system that involves disappearance of LJ particle at lambda=1 in explicit solvent. I ran the simulation at 20 different lambda points ranging from 0 to 1, using soft core potential. In order to use MBAR method (python implementation from Michael shirts ), I have to rerun the simulations, in order to get potential energies for each configuration at every lambda point. Now, here i get into trouble. If i evaluate the trajectories generated at lambda = 1 (particle completely decoupled) using the potential function at lambda = 0, i get very large energy values, which quite likely are responsible for MBAR's failure to converge . The program works well if i calculate free energy to/from an intermediate. ie lambda 0 -> 0.5 and 0.5->1.0 As the potential energies for the configurations generated at lambda=1, evaluated using potential energy function at lambda =0, is expected to be infinite (due to Van der Waals overlaps between solvent and LJ particle), Is it even possible to apply MBAR method to such cases, without splitting the analysis to an intermediate lambda value? Did anyone ran into similar problems, or am i missing something?
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