Cutoff size need not strongly influence molecular dynamics results for solvated polypeptides.
The correct treatment of van der Waals and electrostatic nonbonded interactions in molecular force fields is essential for performing realistic molecular dynamics (MD) simulations of solvated polypeptides. The most computationally tractable treatment of nonbonded interactions in MD utilizes a spherical distance cutoff (typically, 8-12 A) to reduce the number of pairwise interactions. In this work, we assess three spherical atom-based cutoff approaches for use with all-atom explicit solvent MD: abrupt truncation, a CHARMM-style electrostatic shift truncation, and our own force-shifted truncation. The chosen system for this study is an end-capped 17-residue alanine-based alpha-helical peptide, selected because of its use in previous computational and experimental studies. We compare the time-averaged helical content calculated from these MD trajectories with experiment. We also examine the effect of varying the cutoff treatment and distance on energy conservation. We find that the abrupt truncation approach is pathological in its inability to conserve energy. The CHARMM-style shift truncation performs quite well but suffers from energetic instability. On the other hand, the force-shifted spherical cutoff method conserves energy, correctly predicts the experimental helical content, and shows convergence in simulation statistics as the cutoff is increased. This work demonstrates that by using proper and rigorous techniques, it is possible to correctly model polypeptide dynamics in solution with a spherical cutoff. The inherent computational advantage of spherical cutoffs over Ewald summation (and related) techniques is essential in accessing longer MD time scales.
Beck
David A C
DA
Biomolecular Structure and Design Program, University of Washington, Seattle, Washington 98195-7610, USA.
Armen
Roger S
RS
Daggett
Valerie
V
D002942:Circular Dichroism; D003198:Computer Simulation; D006860:Hydrogen Bonding; D046911:Macromolecular Substances / Q000737:chemistry; D008956:Models, Chemical; D008958:Models, Molecular; D010446:Peptide Fragments / Q000737:chemistry; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D012984:Software; D012996:Solutions; D012997:Solvents; D055672:Static Electricity; D013816:Thermodynamics
D046911:Macromolecular Substances; D010446:Peptide Fragments; D010455:Peptides; D012996:Solutions; D012997:Solvents