The CHARMM27 all‐atom force field for nucleic acids represents a highly optimized model
for investigations of nucleic acids via empirical force field calculations. The force field …

In the last five years we have witnessed a significant increase in the number publications
describing accurate and reliable all‐atom molecular dynamics simulations of nucleic acids …

Empirical force‐field calculations on biological molecules represent an effective method to
obtain atomic detail information on the relationship of their structure to their function. Results …

Molecular dynamics simulations based on empirical force fields can greatly enhance
knowledge of DNA and RNA structure and dynamics in solution. Presented are results on …

Improvements in the CHARMM all-atom force field for atomic-level molecular simulations of
lipids are reported. Substantial adjustments have been made to the Lennard-Jones (LJ) …

We review molecular dynamics simulations of nucleic acids, including those completed from
1995 to 2000, with a focus on the applications and results rather than the methods. After the …

Long-range interactions are known to play an important role in highly polar biomolecules
like DNA. In molecular dynamics simulations of nucleic acids and proteins, an accurate …

Recent developments have been made in modeling double-helical DNA at four levels of
three-dimensional structure: the all-atom level, whereby an oligonucleotide duplex is …

Molecular dynamics simulations on DNA and RNA that include solvent are now being
performed under realistic environmental conditions of water activity and salt. Improvements …

Aromatic stacking of nucleic acid bases is one of the key players in determining the structure
and dynamics of nucleic acids. The arrangement of nucleic acid bases with extensive …