I created a single DGDG molecule (digalactosyldiacylglycerol) in Pymol.

The next step is:

Once structure of first molecule is prepared, it must be aligned

so that its main axis is parallel to the z-direction, e.g., acyl chains

along z-axis, so the head group is placed down in the absolute

reference system (this direction is the one assumed in this

example for the initial DPPC molecule). In order to simplify

this and the following steps it is a good practice to draw the acyl

chains in their extended positions and parallel one to the other,

so that the lipid takes the minimum space in the xy-plane.

$ editconf -f DPPC.pdb -o DPPC_rot.gro -rotate X Y Z -box

0.96 0.96 2.20

(a) “X,” “Y,” and “Z” are degrees of rotation around each axis

and they depend on the original positioning of the DPPC

molecule when drawn. Often the correct values for “X,”

“Y,” and “Z” are found through a process of trial and error.

For example my coordinates at the end of acyl chain (atom C51)is:

x=-14.720 y=-7.537 z=9.164

and my coordinates of atom in head group (for example atom C13) is:

x=-14.931 y=19.131 z=2.012

Which rotation can be the best in that example? I think probably y should be minus in head group, so I can create a down-layer. X probably is ok, but Z?

gmx editconf -f DPPC.pdb -o DPPC_rot.gro -rotate 0 180 ?Z? -box

0.96 0.96 2.20

I use this article for guide to modelling bilayer Article Molecular Dynamics Simulations of Lipid Bilayers: Simple Rec...