The Impact of Using Single Atomistic Long-Range Cutoff Schemes with the GROMOS 54A7 Force Field

With
the recent increase in computing power, the molecular modeling
community is now more focused on improving the accuracy and overall
quality of biomolecular simulations. For the available simulation
packages, force fields, and all other associated methods used, this
relates to how well they describe the conformational space and thermodynamic
properties of a biomolecular system. The parameter sets of GROMOS
force fields have been parametrized and validated with the reaction
field (RF) method using charge groups and a twin-range cutoff scheme
(0.8/1.4 nm). However, the most recent versions of GROMACS (since
v.2016) discontinued the support for charge groups. To take full advantage
of the newer and faster versions of this software package with GROMOS
54A7 and RF, we need to evaluate the impact of using a single cutoff
scheme (vs twin-range) and of using the Verlet list update method
(which is atomistic) compared to the group-based cutoff scheme. Our
results show that the GROMOS 54A7 force field seems consistent with
a single cutoff, since the resulting conformation and protonation
ensembles were indistinguishable. The GROMOS parametrization procedure
was also reproduced using an atomistic cutoff scheme, and we have
observed that the hydration free energy values of small amino acid
side-chain analogues were similar to the ones obtained with the group-based
protocol. We do observe a small impact of the atomistic cutoff scheme
in the conformational space of the model systems studied (G1-PAMAM
and DMPC). However, since the structural properties of these systems
are well converged for the cutoff range used (1.4–2.0 nm),
unlike with the group-based cutoff schemes, we are confident that
the atomistic cutoff can be adopted with RF for MD and constant-pH
MD biomolecular simulations using the GROMOS 54A7 force field.