United-Atom Acyl Chains for CHARMM Phospholipids

@article{citeulike:2878235, abstract = {Abstract: In all-atom simulations of lipid membranes, explicit hydrogen atoms contained in the hydrocarbon region are described by a large number of degrees of freedom, although they convey only limited physical information. We propose an implicit-hydrogen model for saturated and monounsaturated acyl chains, aimed at complementing the all-atom CHARMM27 model for phospholipid headgroups. Torsional potentials and nonbonded parameters were fitted to reproduce experimental data and free energy surfaces of all-atom model systems. Comparative simulations of fluid-phase POPC bilayers were performed using the all-hydrogen force field and the present model. The hybrid model accelerates a typical bilayer simulation by about 50\% while sacrificing a minimal amount of detail with respect to the fully atomistic description. In addition, the united-atom description is energetically compatible with all-atom CHARMM models, making it suitable for simulations of complex membrane systems.}, address = {Center for Molecular Modeling, Department of Chemistry, University of Pennsylvania, 231 S. 34th Street, Philadelphia, Pennsylvania 19104-6323, and Research Institute for Computational Sciences, National Institute of Advanced Industrial Science and Technology (AIST), Central 2, 1-1-1, Umezono, Tsukuba, Ibaraki 305-8568, Japan}, author = {H\&\#xe9;nin, Je\&\#x301;r\&\#xf4;me and Shinoda, Wataru and Klein, Michael L. }, citeulike-article-id = {2878235}, doi = {10.1021/jp800687p}, journal = {J. Phys. Chem. B}, keywords = {biomembranes, molecular\_dynamics, molecular\_simulation}, month = {June}, number = {23}, pages = {7008--7015}, posted-at = {2008-07-09 11:35:52}, priority = {0}, title = {United-Atom Acyl Chains for CHARMM Phospholipids}, url = {http://dx.doi.org/10.1021/jp800687p}, volume = {112}, year = {2008} }

TY - JOUR ID - citeulike:2878235 L3 - citeulike-article-id:2878235 TI - United-Atom Acyl Chains for CHARMM Phospholipids JF - J. Phys. Chem. B VL - 112 IS - 23 SP - 7008 EP - 7015 AD - Center for Molecular Modeling, Department of Chemistry, University of Pennsylvania, 231 S. 34th Street, Philadelphia, Pennsylvania 19104-6323, and Research Institute for Computational Sciences, National Institute of Advanced Industrial Science and Technology (AIST), Central 2, 1-1-1, Umezono, Tsukuba, Ibaraki 305-8568, Japan N2 - Abstract: In all-atom simulations of lipid membranes, explicit hydrogen atoms contained in the hydrocarbon region are described by a large number of degrees of freedom, although they convey only limited physical information. We propose an implicit-hydrogen model for saturated and monounsaturated acyl chains, aimed at complementing the all-atom CHARMM27 model for phospholipid headgroups. Torsional potentials and nonbonded parameters were fitted to reproduce experimental data and free energy surfaces of all-atom model systems. Comparative simulations of fluid-phase POPC bilayers were performed using the all-hydrogen force field and the present model. The hybrid model accelerates a typical bilayer simulation by about 50% while sacrificing a minimal amount of detail with respect to the fully atomistic description. In addition, the united-atom description is energetically compatible with all-atom CHARMM models, making it suitable for simulations of complex membrane systems. KW - biomembranes KW - molecular_dynamics KW - molecular_simulation AU - Hénin, Jérôme AU - Shinoda, Wataru AU - Klein, Michael PY - 2008/06/12/ UR - http://dx.doi.org/10.1021/jp800687p ER -