g_permute: Permutation-reduced phase space density compaction

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本程序引自贝尔法斯特女王大学馆藏的CPC程序库（1969-2018年）。 摘要：生物分子过程由自由能变化所支配，其本质依赖于熵与焓之间的精细调控相互作用。由于溶剂分子的扩散运动，蛋白质溶剂化壳层对溶剂化蛋白质的总熵具有至关重要的贡献，而针对该壳层从模拟中精确计算熵值尤具挑战性。据此，针对分子动力学（Molecular Dynamics, MD）轨迹的每一帧，本软件将对溶剂分子进行重新标记，[原文内容截断]。 程序名称：g-permute 目录编号：AECJ_v1_0 待解决问题：从分子动力学模拟轨迹中估算溶剂分子的熵，无法通过普通轨迹直接完成。 Mendeley数据平台的CPC库中收录的本程序版本：AECJ_v1_0；g-permute；10.1016/j.cpc.2008.10.018