Paper Citing NAMD - Abstract
Bhatnagar, Navendu; Kamath, Ganesh; Potoff, Jeffrey J.
Biomolecular Simulations with the Transferable Potentials for Phase Equilibria: Extension to Phospholipids
JOURNAL OF PHYSICAL CHEMISTRY B, 117:9910-9921, AUG 29 2013
The Transferable Potentials for Phase Equilibria (TraPPE) is extended to zwitterionic and charged lipids including phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylserine (PS), and phosphatidylglycerol (PG). The performance of the force field is validated through isothermal-isobaric ensemble (NPT) molecular dynamics simulations of hydrated lipid bilayers performed with the aforementioned head groups combined with saturated and unsaturated alkyl tails containing 12-18 carbon atoms. The effects of water model and sodium ion parameters on the performance of the lipid force field are determined. The predictions of the TraPPE force field for the area per lipid, bilayer thickness, and volume per lipid are within 1-5% of experimental values. Key structural properties of the bilayer, such as order parameter splitting in the sn-2 chain and X-ray form factors, are found to be in close agreement with experimental data.
