Boundary conditions, periodi

MD has been appUed for the determination of changes of physical properties of lipid bilayers caused by the incorporated peptide as well as for the determination of possible peptide stractural alterations. MD were performed under periodie boundary conditions using the GROMACS software [68] and the GROMOS87 [69] forcefield with corrections for hpids [70, 71]. The initial models of transmembrane a-helix peptides have been generated by means of HyperChem [72]. Preequilibrated DMPC and DPPC bilayers with 128 lipid molecules and 3655 molecules of water in L hquid-ciystalline state pubhshed by Tieleman et al. [73] have been used in bilayer modehng. For the simulations with membrane in Lp gel state, we created... 

Fig. 11.1 Example of simulation box for a liquid-liquid interface. Periodie boundary conditions are applied along the three axes. Two liquid-liquid interfaees are obtained...

This progress is encouraging, but some issues still need to be resolved. For materials with periodic boundary conditions or non-collinear magnetism, EBOs will probably be easiest to compute using a modified form of the projector in eqn (5.43) that explicitly accounts for spin degrees of freedom. This will require only the electron and spin density distributions as inputs. Tests also need to be performed to see whether explicit averaging over the hole, as shown in eqn (5.43), increases the EBO accuracy compared with the simplified correlation shown in eqn (5.40). Since eqn (5.40) was only tested for spin unpolarized systems, additional tests need to be performed for spin polarized systems. For non-periodie systems, EBOs computed with proposed projectors should be carefully compared to NAOP bond orders. Because the Kohn-Sham DFT spin-orbitals form a single Slater determinant, the basin EBO has the form... 

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