@article {642, title = {Mixed Atomistic and Coarse-Grained Molecular Dynamics: Simulation of a Membrane-Bound Ion Channel}, journal = {J Phys Chem B}, volume = {110}, number = {31}, year = {2006}, note = {Shi, Qiang Izvekov, Sergei Voth, Gregory A 1 S10 RR17214-01/RR/NCRR NIH HHS/United States R01 GM63796/GM/NIGMS NIH HHS/United States Letter Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov{\textquoteright}t Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. United States The journal of physical chemistry. B J Phys Chem B. 2006 Aug 10;110(31):15045-8.}, pages = {15045-8}, abstract = {

The recently developed multiscale coarse-graining (MS-CG) method (Izvekov, S.; Voth, G. A. J. Phys. Chem. B 2005, 109, 2469; J. Chem. Phys. 2005, 123, 134105) is used to build a mixed all-atom and coarse-grained (AA-CG) model of the gramicidin A (gA) ion channel embedded in a dimyristoylphosphatidylcholine (DMPC) lipid bilayer and water environment. In this model, the gA peptide was described in full atomistic detail, while the lipid and water molecules were described using coarse-grained representations. The atom-CG and CG-CG interactions in the mixed AA-CG model were determined using the MS-CG method. Molecular dynamics (MD) simulations were performed using the resulting AA-CG model. The results from simulations of the AA-CG model compare very favorably to those from all-atom MD simulations of the entire system. Since the MS-CG method employs a general and systematic approach to obtain effective interactions from the underlying all-atom models, the present approach to rigorously develop mixed AA-CG models has the potential to be extended to many other systems.

}, keywords = {*Computer Simulation Dimyristoylphosphatidylcholine/chemistry Gramicidin/*chemistry Ion Channels/chemistry Lipid Bilayers/chemistry Models, Molecular Peptides/*chemistry Protein Conformation Quantum Theory Water/chemistry}, doi = {10.1021/jp062700h}, author = {Shi, Q. and Izvekov, S. and G. A. Voth} }