Suitability of the MARTINI Force Field for Use with Gas-Phase Protein Complexes
1Department of Chemistry, University of British Columbia , 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada.
Abstract:
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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