Biomembranes simulation methods

As it is assured that the conformations generated with the Marcelja field are consistent with experimental data, the procedure employing the overlay method and the continuous Marcelja model is a powerful tool for preparation of the initial coordinates of biomembrane simulations. By applying a short molecular dynamics simulation to the initial coordinates prepared by this procedure, the long equilibration time necessary to obtain results consistent with experiments is well circumvented. 

Marcelja-Radic theory and its extensions (20-22) and Jonsson-Wennerstrom theory and its extensions (15-19) do not address the problem of the hydration force on the level of a detailed molecular Hamiltonian. Due to the complexity of the problem perhaps only a computer simulation technique can provide a description on this level. The tremendous usefulness of computer methods in the study of DNA and protein molecules (30, 31) inspires the hope that simulations will also play an important role in the study of biomembrane molecules. The first computer simulations to study the problem of hydration force on phospholipid molecules were performed by Scott (32, 33) and by Kjellander and Marcelja (34, 35). Because these studies were performed seven to eight years ago, the researchers were limited by the computer power available. As a result, the simulations were performed with... 

Simulations of the actual chemical structures of biomembranes are, of course, eferable to the simpler pioneering simulation. However, the computational burden for actual simulations is very large even for the present high-speed computers. Further, the relaxation process for equilibration starting from the X-ray structure of a crystal is much slower, as more complicated structures are considered. Thus, an elaborate procedure to prepare initial coordinates was developed to avoid the long equilibration time and to obtain more realistic coordinates in an attainable time scale. The procedure is based on generation of a set of conformations of lipids with mean field methods. The n an field methods have been developed... 

Further, the overlay method is also applied for construction of solvated biomembranes with proteins included. A protein is overlay d onto the lipid bilayer coordinates, and the overlapped lipids are omitted. The lipid bilayer including the protein is then overlayed onto a water box. This twice applied overlay method was applied to a simulation of gramicidin A in a solvated lipid bilayer, as shown in Figure 2. Gramicidin... 

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