The impact of using single atomistic long range cutoff schemes with the GROMOS 54A7 force field

Abstract

Due to the recent increase in computing power, the molecular modeling community has been focused on improving the accuracy and overall quality of biomolecular simulations. These technological improvements centered on the development of new force fields and simulation packages, allowed for more complex and heavier systems to be tackled, while maintaining, or even improving simulations speed. Some force fields, such as GROMOS, have been parameterized and validated using a reaction field (RF), charge groups and a twin-range cutoff scheme (0.8 and 1.4 nm) to treat long range electrostatics [1]. However, in GROMACS software package, the use of group-based cutoff scheme will be deprecated in future versions. As to properly use the newer and faster versions of this simulation package coupled with GROMOS 54A7 and RF, it is crucial to assess the impact on the system sampling when using a single atomistic cutoff (based on the Verlet method) instead of the twin-range group-based scheme. We reproduced the GROMOS parameterization procedure [1] with both schemes and measured very similar hydration free energy values of small amino acid side chains analogs between both protocols [2]. However, we observed a small, yet significant, difference on the conformational spaces of G1-PAMAM and DMPC when using the atomistic cutoff scheme [2]. The DMPC Al values decrease to a region outside the experimental range, which is not surprising since the force field parameters were optimized for a group-based scheme. Nevertheless, the structural properties for both systems are better converged for the used atomistic cutoff range (1.4-2.0 nm) relative to the group-based cutoff simulation set [2]. The use of a single atomistic cutoff scheme seems a viable approach for MD simulations of biomolecules using G54A7 force field, even if in some cases, new calibration protocols are needed. (1) Oostenbrink, C.; Villa, A.; Mark, A. E.; van Gunsteren, W. F. A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6. J. Comput. Chem. 2004, 25, 1656–1676 (2) Silva, T. F. D., Vila-Viçosa, D., Reis, P. B. P. S., Victor, B. L., Diem, M., Oostenbrink, C., and Machuqueiro, M. (2018) "The impact of using single atomistic long range cutoff schemes with the GROMOS 54A7 force field", J. Chem. Theory Comput., 14, 5823-5833