Abstract:
The entropy of water molecules plays a dominant role in various biological processes,
like protein folding and molecular recognition. Understanding the dependence of water
entropy on the surface topography and chemistry of biomolecular surfaces is necessary
to comprehend these processes. However, calculating water entropy from molecular dy-
namics simulation remains challenging due to the difficulty in sampling the large phase
space, even for a small system of water molecules within realistic time scales. Here, we
use the Single Water Entropy (SWE) approach to calculate water entropy, which utilizes
Permutation Reduction (PR) to reduce the phase space volume accessible to water. The
initial work involved the calculation of water entropy around homogeneous hydrophobic
model surfaces. Subsequently, our work was extended to incorporate chemistry in our
systems. We also calculated the dynamical properties of water molecules like velocity
and rotational autocorrelation functions.
