This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Keywords: peptide lipid, bilayers, molecular dynamics Abstract: This proposal seeks to understand the POPC bilayer system in some detail by the use of molecular dynamics simulations. We have performed a multi-nanosecond simulation of a POPC bilayer (20,000 atoms) with periodic boundary conditions and Ewald sums using CHARMM. The results will be analyzed in terms of dipole fluctuations which may aid in understanding of the electrostatic response properties of the system. Additionally we are performing relatively free energy calculations for several sidechain analogs as a function of the position relative to the bilayer normal. The resulting transfer free energy curves should help with understanding permeation of drugs and small peptides and aid construction of mean field models of the bilayer setting.
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