<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:12pt"><div>Dear All,<br>
<br>
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.<br>
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.<br>
<br>
There are two options for treating long-range electrostatic interactions for my system:<br>
(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)<br>
<br>
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).<br>
<br>
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.
<br>
<br>
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.<br>
<br>
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!<br><br>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?<br><br>Sorry for so many questions, thanks for your time! <br><br>best regards,<br>
Jianguo<br>
Postdoc Research Fellow<br>Bioinformatics Institute and Singapore Eye Research Institute, Singapore<br>
<br>
<br>
<br>
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