Paper Citing NAMD - Abstract
Poghosyan, A. H.; Yeghiazaryan, G. A.; Gharabekyan, H. H.; Koetz, J.; Shahinyan, A. A.
A molecular dynamics study of Na-dodecylsulfate/water liquid crystalline phase
MOLECULAR SIMULATION, 33:1155-1163, 2007
We have performed a Series of long (about 130 ns) molecular dynamics simulations of a sodium dodecylsulfate/water liquid crystalline (LC) phase, consisting of 512 sodium dodecylsulfate and 15,000 water molecules, where the initial starting configuration is varied. In addition, the all atom and the united atom model were compared using NAMD and GROMACS codes with CHARMM27 and modified GROMOS87 force fields, respectively. Characteristic parameters, such as area per molecule, bilayer thickness, roughening, and orientation of the hydrocarbon chains in the hydrophobic core of the bilayer have been calculated. In general, the data obtained by means of molecular dynamics simulation are in agreement with the experimental X-ray diffraction data. However, only for the all-atom model, we found an excellent agreement with the experimental values of area per molecule and hydrocarbon chain packing parameters. Therefore, one can conclude that the use of a CHARMM27 all-atom force field, implemented in NAMD code, is the best approach for simulations of a SDS LC-phase.
