A user‐friendly, Python‐based quantum mechanics/Gromacs interface: gmx2qmmm

Abstract

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.

Impact of structural sampling, coupling scheme and state of interest on the energy transfer in CP29

“…Note that due to our model only including CP29, Chl a 616, which is at the interface to the PSII CP47 antenna, was not considered. The QM/MM calculations were performed with the gmx2qmmm interface 59 using Gaussian 16 60 and the GROMACS simulation package 2018.6 61 . All QM and QM/MM calculations employed the CAM-B3LYP functional with the 6-31G* basis set; the force field was in all cases AMBER99SB*-ILDNP.…”

Impact of Structure, Coupling Scheme, and State of Interest on the Energy Transfer in CP29

“…Note that due to our model only including CP29, Chl a 616, which is at the interface to the CP47 antenna of the photosystem core complex, was not considered. The QM/MM calculations were performed with the gmx2qmmm interface using Gaussian 16 and the GROMACS simulation package 2018.6 . All QM and QM/MM calculations employed the CAM-B3LYP functional with the 6-31G* basis set; the force field was in all cases AMBER99SB*-ILDNP …”

Germany’s Future in Theoretical and Computational Chemistry: a Special Issue Celebrating DEAL

“…However, a full quantum treatment of electrons and nuclei is not always necessary and techniques like QM/MM or full MM can be employed. For example, Götze et al [14] present a new QM/MM software interface (gmx2qmmm), that offers novel ways to treat the QM/MM boundary region, showing how it fares for flexible amino‐acid conformations and the calculation of UV/vis spectra. Finally, Oldamur Hollóczki [15] investigates the stability of oligoalanines in the presence of plastic nanoparticles through simulated annealing and semi‐empirical approaches for the conformational search and stability assessment, respectively.…”