g_permute: Permutation-reduced phase space density compaction

Abstract

Biomolecular processes are governed by free energy changes and thus depend on a fine-tuned interplay between entropy and enthalpy. To calculate accurate values for entropies from simulations is particularly challenging for the solvation shell of proteins, which contributes crucially to the total entropy of solvated proteins, due to the diffusive motion of the solvent molecules. Accordingly, for each frame of a Molecular dynamics (MD) trajectory, our software relabels the solvent molecules, su...