A user-friendly, Python-based quantum mechanics/Gromacs interface: gmx2qmmm
Götze, Jan P. and Pi, Yuan-Wei and Petry, Simon and Langkabel, Fabian and Witte, Jan Felix and Lemke, Oliver – 2020
We introduce a Python 2.7 software called gmx2qmmm, which provides an interface between the Gaussian and Gromacs software packages in an additive quantum mechanics/molecular mechanics (QM/MM) scheme. Other QM packages will be added in future releases. The main advantage of gmx2qmmm is its simplicity in terms of input setup and configuration as it maintains the Gromacs file formats, as well as input conventions. It is also designed such that users do not need to reconfigure or recompile any of the interfaced programs. While our main goal was to provide a simplified transition from Gromacs to QM/MM using Gromacs directly as the basis for the MM part, we considered alternative ways to treat the QM/MM boundary. Our software was also developed to test a previously considered way to account for the presence of link atoms, which we term here link atom correction functions (LCFs). We show that LCFs can be good candidates to improve the forces at the QM/MM junction; however, from our data, it is also apparent that LCFs will not necessarily improve energy barriers, likely due to them being tailored to improve the situation close to potential minima. LCFs are, however, trivial to set up and can be used in the future to support the accuracy of QM/MM optimizations and dynamics. We present data on how our interface compares to a full QM description of small polypeptides; furthermore, we investigate the UV/vis spectroscopy of chlorophyll-containing proteins depending on the employed potentials and geometries.