  Over the past decades, molecular dynamics (MD) simulations of biomolecules
have become a mainstream biophysics technique. As the length and time scales
amenable to the MD method increase, shortcomings of the empirical force
fields---which have been developed and validated using relatively short
simulations of small molecules---become apparent. One common artifact is
aggregation of water-soluble biomolecules driven by artificially strong
charge--charge interactions. Here, we report a systematic refinement of
Lennard-Jones parameters (NBFIX) describing amine--carboxylate and
amine--phosphate interactions, which brings MD simulations of basic
peptide-mediated nucleic acids assemblies and lipid bilayer membranes in better
agreement with experiment. As our refinement neither affects the existing
parameterization of bonded interaction nor does it alter the solvation free
energies, it improves realism of an MD simulation without introducing
additional artifacts.
