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Study of the electrostatics treatment in molecular dynamics simulations
Author(s) -
Garemyr Robert,
Elofsson Arne
Publication year - 1999
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/(sici)1097-0134(19991115)37:3<417::aid-prot9>3.0.co;2-u
Subject(s) - molecular dynamics , cutoff , dielectric , statistical physics , force field (fiction) , periodic boundary conditions , electrostatics , smoothing , stability (learning theory) , range (aeronautics) , constant (computer programming) , physics , boundary value problem , computer science , chemistry , computational chemistry , materials science , quantum mechanics , machine learning , programming language , composite material , computer vision
This article considers the treatment of long‐range interactions in molecular dynamics simulations. We investigate the effects of using different cutoff distances, constant versus distance‐dependent dielectric, and different smoothing methods. In contrast to findings of earlier studies, we find that increasing the cutoff over 8 Å does not significantly improve the accuracy (Arnold and Ornstein, Proteins 1994;18:19–33), and using a distance‐dependent dielectric instead of a constant dielectric also does not improve accuracy (Guenot and Kollman, Protein Sci 1992;1:1185–1205). This might depend on differences in simulation protocols or force fields, or both, because we use the CHARMM22 force field with stochastic boundary conditions, whereas earlier studies used other protocols and energy functions. We also note that the stability of the simulations is highly dependent on the starting structure, showing that accurate molecular simulations not only depend on a realistic simulation protocol but also on correct initial conditions. Proteins 1999;37:417–428. ©1999 Wiley‐Liss, Inc.