Lipid Collection

In this page you will find a collection of all lipids currently available in GNOMM.

Note that the following tables indicate whether a lipid is available for CHARMM, GROMOS, MARTINI or PACE. An effort has been made to include as many lipids as possible for each force field, taking into account known information on the membrane composition of Gram-negative bacteria. However, not all lipids are available in all force fields. Specifically, in GROMOS most glycerophospholipids are phosphatidyl-cholines (PCs) and other lipid categories are under-represented. In the case of Martini, note that due to the "fuzzy" nature of Coarse-Graining, all-atom lipid with similar tail length and geometry are often represented by the same CG lipid topology; for example, in Martini the so-called "DPPC" lipid actually represents all lipids with tails ranging from 16:0 to 18:0 and can represent both DPPC and DSPC (for more information, please refer to the Martini Lipidome). Finally, in the case of the PACE, note that the force field uses the MARTINI CG model to represent the lipids and solvents. Therefore, all standard phospholipids available in MARTINI also exist in PACE. As far as LPSs are concerned, PACE parameters are available for all variants of Lipid A, as well as the PAO1 LPS.

Using the following tables as a guide, choose the force field that best satisfies your system's needs when using the GNOMM membrane builder services.

Lipopolysaccharides (LPSs)

Phospholipids