Cutoff size does strongly influence molecular dynamics results on solvated polypeptides

Area of Science:

• Computational Chemistry
• Biophysics
• Molecular Modeling

Background:

• Molecular dynamics (MD) simulations are vital for studying biomolecular behavior.
• Accurate treatment of Coulomb interactions is essential for reliable MD results.
• The choice of cutoff radius significantly influences simulation outcomes.

Purpose of the Study:

• To investigate the impact of different cutoff radii on Coulomb interactions in MD simulations.
• To assess the stability of a model peptide's alpha-helix under varying cutoff conditions.
• To compare cutoff-based methods with the Ewald summation technique.

Main Methods:

• Molecular dynamics simulations of a 17-residue peptide with explicit water molecules.
• Analysis of Coulomb interactions using cutoff radii of 0.6, 1.0, and 1.4 nm.
• Comparison with simulations employing the Ewald summation technique.

Main Results:

• Alpha-helix stability was dependent on the cutoff radius used.
• A 1.0 nm cutoff partially conserved helix stability, while a 1.4 nm cutoff led to rapid destabilization.
• Ewald summation simulations maintained helical character, unlike the 1.4 nm cutoff trajectory.
• The commonly used 1.0 nm cutoff is insufficient for ensuring Coulomb interaction convergence.

Conclusions:

• Simple cutoff schemes for Coulomb interactions are questionable for solvated biomolecules.
• A cutoff radius of 1.4 nm is inadequate for accurate MD simulations.
• Ewald summation provides a more reliable approach for handling long-range electrostatic interactions in biomolecular simulations.