g_permute: Permutation-reduced phase space density compaction

Published: 1 March 2009| Version 1 | DOI: 10.17632/6zj7wzj9dg.1
F. Reinhard, O.F. Lange, J.S. Hub, J. Haas, H. Grubmüller


This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018) 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... Title of program: g-permute Catalogue Id: AECJ_v1_0 Nature of problem Estimating the entropy of solvent molecules from a molecular dynamics simulation trajectory cannot be performed on ordinary trajectories. Versions of this program held in the CPC repository in Mendeley Data AECJ_v1_0; g-permute; 10.1016/j.cpc.2008.10.018



Molecular Biology, Biological Sciences, Computational Physics, Computational Method