Paper Citing NAMD - Abstract
Poghosyan, Armen H.; Gharabekyan, Hrant H.; Shahinyan, Aram A.
Molecular dynamics simulations of DMPC/DPPC mixed bilayers
INTERNATIONAL JOURNAL OF MODERN PHYSICS C, 18:73-89, JAN 2007
We have performed the atomistic MD simulation of dimyristoylphosphatidylcholine(DMPC)/dipalmitoylphosphatidylcholine(DPPC ) mixed bilayers, consisting of various fraction of lipids, i.e., with fraction 0.25, 0.5 and 0.75 and hydration level 33 water molecules per lipid. The simulations were performed using NAMD code. The area per lipid, densities, orientational order parameters and tilt angle of hydrocarbon chain and also the interdigitation of chains were calculated. It has been established that the interdigitation degree of hydrocarbon chains is increased as the DPPC fraction is decreased. It has been also stated that the area per lipid value in case of racemic mixtures is about 0.72 nm(2), which is in good agreement with experimental estimations. The hydrocarbon thickness is increased as the DPPC fraction increased. The DMPC/DPPC mixtures behave as almost ideally mixtures. The diffusion coefficients were also calculated and the results are in agreement with experimental findings. All the calculated parameters were compared with values obtained either from experimental data of DPPC or DMPC depending on the fraction of compound. The reason is that there are no experimental findings on DMPC/DPPC mixtures.
