Rotational Effects on Free Energy Landscapes of Diffusing Molecules in Coarse-Grained Models*

Accurate coarse-grained modeling of the dynamics of macromolecules with a Generalized Langevin Equation (GLE) requires detailed knowledge of the intramolecular potential of mean force and friction coefficients, which are usually calculated from the analysis of an atomistic simulation.

We demonstrate that the free energy landscape of a diffusing molecule can be distorted by the coupling of internal fluctuations with centrifugal forces. We show how corrections for the rotational entropy affect the potential of mean force and illustrate the formal procedure needed to isolate the correct potential energy surface from the measured one.

Furthermore, we show that these corrections to the modeled potential are, in principle, necessary in order to recover accurate site-specific friction coefficients from the time-lagged correlations of the forces in the GLE. These methods are demonstrated on a toy model of a two-state trimer with exponential memory, showing that the total integral of the memory function and the related friction coefficients can be accurately recovered from an observed trajectory of this system.