Journal
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
Volume 8, Issue 4, Pages 1304-1313Publisher
AMER CHEMICAL SOC
DOI: 10.1021/ct200739s
Keywords
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Funding
- Natural Sciences and Engineering Research Council (NSERC) of Canada
- Canada Foundation for Innovation, Alberta Innovation and Science, BC Advanced Education
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The MARTINI coarse-grained force field [Monticelli, L. et al. J. Chem. Theory Comput. 2008, 4, 819-834] is examined for use in molecular dynamics simulations of the dissociation of gas-phase protein complexes. Coarse-grained force fields allow longer time scales and larger systems to be treated compared with all-atom force fields. In this work, results for the dissociation of the cytochrome c' dimer using MARTINI are compared with published studies using the OPLS-AA/L all-atom force field. Several structural parameters such as the minimum distance between monomers, radius of gyration, and root-mean-square deviation as well as potential energy contributions (Lennard-Jones and Coulomb) are calculated as a function of the center of mass distance. The MARTINI force field semiquantitatively reproduces the results of previous all-atom studies but appears to be somewhat too attractive.
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