Paper Citing NAMD - Abstract
Curtis, Emily M.; Hall, Carol K.
Molecular Dynamics Simulations of DPPC Bilayers Using "LIME", a New Coarse-Grained Model
JOURNAL OF PHYSICAL CHEMISTRY B, 117:5019-5030, MAY 2 2013
A new intermediate resolution model for phospholipids, LIME, designed for use with discontinuous molecular dynamics (DMD) simulations is presented. The implicit solvent model was developed using a multiscale modeling approach in which the geometric and energetic parameters are obtained by collecting data from atomistic simulations of a system composed of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) molecules and explicit water. In the model, 14 coarse-grained sites that are classified as 1 of 6 types represent DPPC. DMD simulations performed on a random solution of DPPC. resulted in the formation of a defect-free bilayer in less than 4 h. The bilayer formed quantitatively reproduces the main structural properties (e g, area per lipid, bilayer thickness;. bond order parameters) that are observed. experimentally. In addition, the bilayer transitions from a liquid-crystalline phase to a tilted gel phase when the temperature is reduced Transbilayer movement of a lipid from the bottom leaflet to the top leaflet is the temperature is increased.
