Laboratory of Numerical Simulation of Chemical Systems (LABSIN), Departments of Chemical Engineering (EQA), Federal University of Santa Catarina (UFSC), 88040-900 Florianópolis, SC, Brazil.
Group of Chemical and Biochemical process, Departament of Chemical and Environmental engineering, Universidad Nacional de Colombia (UNAL), Cra 30 # 45-03, 11021 Bogota, Colombia.
J Phys Chem A. 2023 Feb 16;127(6):1555-1563. doi: 10.1021/acs.jpca.2c08335. Epub 2023 Feb 7.
Molecular simulation users are sometimes discouraged from using specific molecular models because of the inconvenience of finding the force field parameters and preparing and validating the topology files. To facilitate this process and make the accurate anisotropic force field AUA4 available to molecular dynamics users, we have created and validated an automated topology and coordinate file creation routine for the GROMACS molecular simulation software. In the present work, we describe the AUA4, explain its particularities and how it was implemented, thoroughly validating the implementation, and for the first time, perform a molecular dynamics benchmark for this transferable force field. Several properties were computed, namely, liquid density, vapor pressure, and vaporization enthalpy by conducting explicit vapor-liquid interface simulations. The results evidence the correct implementation showing slight deviations from the parametrization studies. The benchmark shows the superior predictive capability of the AUA4 in recreating liquid density (RMSD equal to 17.0 kg/m) and vaporization enthalpy (RMSD equal to 1.3 kJ/mol) compared to other transferable force fields. In addition, its superior computational time performance doubles or even triples compared to an all-atom force field such as the OPLS, depending on whether the workstation counts with GPU.
分子模拟用户有时会因为难以找到力场参数以及准备和验证拓扑文件而对使用特定分子模型感到沮丧。为了方便这一过程，并使准确的各向异性力场 AUA4 可供分子动力学用户使用，我们为 GROMACS 分子模拟软件创建并验证了一个自动化拓扑和坐标文件创建例程。在本工作中，我们描述了 AUA4，解释了其特殊性以及如何实现它，彻底验证了实现，并首次对这个可转移力场进行了分子动力学基准测试。通过进行显式气液界面模拟，计算了几个性质，即液体密度、蒸气压和蒸发热。结果表明，实现方式正确，仅略有偏离参数化研究。基准测试表明，AUA4 在重现液体密度（RMSD 等于 17.0 kg/m）和蒸发热（RMSD 等于 1.3 kJ/mol）方面具有优越的预测能力，优于其他可转移力场。此外，与全原子力场（如 OPLS）相比，其优越的计算时间性能提高了一倍甚至三倍，具体取决于工作站是否配备 GPU。
