Dear All, I am working on the interaction of a positively charged peptide (18AA) and the bacterial membrane consisting of a mixture of zitterionic and negatively charged lipids. Our experiments show that the peptide can disrutp the membrane. One problem puzzed me is that which method to use in treating the long-range electrostatic interactions for my system. The following is my understanding, please correct me if I am wrong.
There are two options for treating long-range electrostatic interactions for my system: (a) use a normal 3-D PME (by setting ewald_geometry=3d, which is the defaut option); and (b) use a slab PME in 2-D by setting ewald_geometry=3dc (thanks for David Bostick's suggestions) If I use normal PME in 3-D (ewald_geometry=3d), and put the peptide on top of the membrane, I cannot increase the peptide concentration. For example, if I put 3 peptide on top of the membrane, 1 peptide will move to the lower leaflet of top image box. I believe this is because of the repulsion between the peptide and also the attraction between the peptide and the lower leaflet of the membrane in the top image box. Also as mentioned in the previous posts, 3D PME has artifact (i.e., due to the dipole moment of the simulation box which is significant as pointed out by David Bostick through emails since I have a positively charged peptide and a negatively charged membrane). When using 2D PME with slab geometry (ewald_geometry=3dc), the membrane is treated as an infinite charged slab, the positively charged peptide is not only interacts with the membrane in the central box, but also interacts with the membrane in the image boxes. Although the interaction between the peptide and the membrane in the image boxes far from the central box is very weak, but the overal sum of all these interactions could be very strong since there are infinite number of image boxes. Therefore it will over-estimate the intearction betwen the peptide and the membrane. In fact, I got very different results when setting ewald_geometry being 3d or 3dc. Using ewald_geometry=3d, nothing happens except a minor deformation of the membrane in the vicinity of the peptide. However, when using ewald_geometry=3dc, the peptide readily induce a water pore and penetrate into the membrane. I am not sure if the results using 2d PME is correct or not, as it has some artifact for my system. I am wondering how big the artifact is due to the infinity of the 2D PME for slab geometry. Any suggestions for modeling the finite size of the cell membrane are appreciated! Another question is about the parameter epsilong_surface in Gromacs which is the dipole correction of Ewald summation. Is it suitable to use this parameter in my simulations? If possible, which value I need to use for this parameter? Sorry for so many questions, thanks for your time! best regards, Jianguo Postdoc Research Fellow Bioinformatics Institute and Singapore Eye Research Institute, Singapore
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