Thermodynamic
stability assessment of nanocrystal systems requires
precise free energy calculations. This study highlights the importance
of meticulous control over various factors, including the thermostat,
time step, potential cutoff, initial configuration, sampling method,
and overall simulation duration. Free energy computations in dry (solvent-free)
systems are on the order of several hundred k
B
T but can be obtained with consistent accuracy.
However, calculation of internal energies becomes challenging, as
they are typically much larger in magnitude than free energies and
exhibit significant noise and reduced reliability. To address this
limitation, we propose a new internal energy estimate that drastically
reduces the noise. We also present formulas that enable the optimization
of the parameters of the harmonic bias potential for optimal convergence.
Finally, we discuss the implications of these findings for the computation
of free energies in nanocrystal clusters and superlattices.