GeneralRequirements

General requirements

• The membrane's normal must be aligned to Z axis.
• All tools require that trajectories are wrapped according to periodic boundary conditions. Trajectories can be wrapped at run-time setting the “Wrap command” (or "-wrapcmd" command line parameter). Wrapping requires periodic box information to be available in the trajectory.
  
• Molecules must not be broken at the periodic boundary box.
  
• Assignments of lipids to either leaflet is based on which side of the bilayer's center of mass they happen to be. Make sure the lipids are properly wrapped in the Z direction. Extremly deformed membranes may lead also to leaflet assignment issues.
  
• Connectivity is expected for the whole system. This is ensured by loading the system's topology file, usually a .psf (CHARMM) or .prmtop (AMBER) topology. This is especially true for the -S_CD order parameter tool.
  • PDB files can generally not be used as topology files, because connectivity information is inferred from distances and types only approximately.
  • GROMACS users may be able to Gromacs topology files to .psf files with the top2psf script.

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