Schedule Jun 08, 2012
Suitability of the MARTINI Force Field For Use With Gas-Phase Protein Complexes
Mark Thachuk (UBC)

Authors: Sarah K. Fegan and Mark Thachuk

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 average forces are calculated as a function of center of mass distance. The MARTINI force field semi-quantitatively reproduces the results of previous all-atom studies but appears to be somewhat too attractive.

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