Department of Chemistry, Lehman College, 205 W Bedford Pk Blvd, Bronx, New York, 10468.
Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York, New York, 10016.
J Comput Chem. 2016 Aug 5;37(21):2029-37. doi: 10.1002/jcc.24417. Epub 2016 Jun 18.
The expulsion of water from surfaces upon molecular recognition and nonspecific association makes a major contribution to the free energy changes of these processes. In order to facilitate the characterization of water structure and thermodynamics on surfaces, we have incorporated Grid Inhomogeneous Solvation Theory (GIST) into the CPPTRAJ toolset of AmberTools. GIST is a grid-based implementation of Inhomogeneous Fluid Solvation Theory, which analyzes the output from molecular dynamics simulations to map out solvation thermodynamic and structural properties on a high-resolution, three-dimensional grid. The CPPTRAJ implementation, called GIST-cpptraj, has a simple, easy-to-use command line interface, and is open source and freely distributed. We have also developed a set of open-source tools, called GISTPP, which facilitate the analysis of GIST output grids. Tutorials for both GIST-cpptraj and GISTPP can be found at ambermd.org. © 2016 Wiley Periodicals, Inc.
水从表面的排出，基于分子识别和非特异性结合，对这些过程的自由能变化有重大贡献。为了促进表面上水结构和热力学的表征，我们已将非均匀网格溶剂化理论（GIST）纳入 AmberTools 的 CPPTRAJ 工具集中。GIST 是不均匀流体溶剂化理论的网格实现，它分析分子动力学模拟的输出，在高分辨率的三维网格上绘制溶剂化热力学和结构性质。名为 GIST-cpptraj 的 CPPTRAJ 实现具有简单易用的命令行界面，是开源和免费分发的。我们还开发了一组名为 GISTPP 的开源工具，用于简化 GIST 输出网格的分析。GIST-cpptraj 和 GISTPP 的教程可在 ambermd.org 上找到。© 2016 威利父子公司
