Merz Pascal T, Hsu Wei-Tse, Thompson Matt W, Boothroyd Simon, Walker Chris C, Shirts Michael R
Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80309, United States of America.
Boothroyd Scientific Consulting Ltd., 71-75 Shelton Street, London, United Kingdom.
J Open Source Softw. 2022;7(69). doi: 10.21105/joss.03981. Epub 2022 Jan 6.
Molecular simulations such as molecular dynamics (MD) and Monte Carlo (MC) simulations are powerful tools allowing the prediction of experimental observables in the study of systems such as proteins, membranes, and polymeric materials. The quality of predictions based on molecular simulations depend on the validity of the underlying physical assumptions. physical_validation allows users of molecular simulation programs to perform simple yet powerful tests of physical validity on their systems and setups. It can also be used by molecular simulation package developers to run representative test systems during development, increasing code correctness. The theoretical foundation of the physical validation tests were established by Merz & Shirts (2018), in which the physical_validation package was first mentioned.
诸如分子动力学（MD）和蒙特卡洛（MC）模拟之类的分子模拟是强大的工具，可用于预测蛋白质、膜和聚合物材料等系统研究中的实验可观测值。基于分子模拟的预测质量取决于基础物理假设的有效性。物理验证允许分子模拟程序的用户对其系统和设置进行简单而强大的物理有效性测试。分子模拟软件包开发人员也可以在开发过程中使用它来运行具有代表性的测试系统，从而提高代码的正确性。物理验证测试的理论基础由Merz和Shirts在2018年建立，其中首次提到了物理验证软件包。
