Paper Citing NAMD - Abstract
Klauda, Jeffery B.; Eldho, Nadukkudy V.; Gawrisch, Klaus; Brooks, Bernard R.; Pastor, Richard W.
Collective and noncollective models of NMR relaxation in lipid vesicles and multilayers
JOURNAL OF PHYSICAL CHEMISTRY B, 112:5924-5929, MAY 15 2008
NMR C-13 spin lattice relaxation (1/T-1) rates of dipalmitoylphosphatidylcholine (DPPC) bilayers obtained from molecular dynamics simulations of 72 and 288 lipids are compared with each other, with experimental values from large liposomes obtained by magic angle spinning, and with previously published experimental data from small vesicles. The experimental results for multilayers and vesicles at the same frequencies differ only slightly. The simulation results indicate that T-1 relaxation in the 15.1 to 201.2 MHz carbon frequency range and up to 100 angstrom length scale is dominated by fast isomerizations and slower lipid wobble (D-perpendicular to approximate to 2.5 x 10(8) s(-1)). Rotational diffusion about the lipid long axis (described by D-parallel to) does not make a substantial contribution to the T-1. Modifications to the acyl chain torsional potential energy function used for the simulations substantially improve agreement with experiment.
