On the Ewald artifacts in computer simulations. The test-case of the octaalanine peptide with charged termini.
The treatment of electrostatic interactions in molecular simulations is of fundamental importance. Ewald and related methods are being increasingly used to the detriment of cutoff schemes, which are known to produce several artifacts. A potential drawback of the Ewald method is the spatial periodicity that is imposed to the system, which could produce artifacts when applied in the simulation of liquids. In this work we analyze the octaalanine peptide with charged termini in explicit solvent, for which severe effects due to the use of Ewald sums were predicted using continuum electrostatics. Molecular Dynamics simulations for a total of 158 nanoseconds were performed in cells of different sizes. From the comparison of the results of different system sizes, no significant periodicity-induced artifacts were observed. It is argued that in current biomolecular simulations, the incomplete sampling is likely to affect the results to a larger extent than the artifacts induced by the use of Ewald sums.
Villarreal
Marcos Ariel
MA
Departamento de Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, CIQUIBIC (CONICET), Pabellón Argentina, Ciudad Universitaria, CP 5000 Córdoba, Argentina. arloa@dqb.fcq.unc.edu.ar
Montich
Guillermo Gabriel
GG
D000409:Alanine / Q000737:chemistry*; D003198:Computer Simulation; D008958:Models, Molecular; D010446:Peptide Fragments / Q000737:chemistry*; D011487:Protein Conformation
D010446:Peptide Fragments; D000409:Alanine