Molecular dynamics simulations of proteins in solution: Artifacts caused by the cutoff approximation

Abstract

Molecular dynamics (MD) simulations of human lysozyme in water were carried out for 400 ps with/without the truncation of long-range Coulomb interactions in order to investigate artificial effects caused by the cutoff method. MD simulations with the long-range Coulomb interactions included were carried out by using a recently developed method [PPPC method; Mol. Simul. 8, 321 (1992)]. On the other hand, MD simulations with the long-range Coulomb interactions truncated were carried out using the 10 Å cutoff method. Comparing both results, the following artifacts were found. The cutoff method caused a 1.7 Å larger deviation of charged residues from the x-ray structure than the PPPC method. Further, the cutoff method caused unacceptably large fluctuation around the equilibrium structure in water. However, the fluctuation found with the PPPC method correlated well with that derived from x-ray B-factors.