7.3. Changing Granularity / Coarse Graining
This mode can be activated by using the left tab inside the Molecule Editor. Basically, you can select a group of atoms and combine them into one single particle. Additionally, this particle, as well as single atoms can be assigned with some further identifiers.
In order to wrap a group of atoms into a particle, you'll need to pick the atoms. With the left mouse button you can select/deselect single atoms or you can use a rubberband selection by holding down the ALT-key:
Once your selection is done, press 'Combine to Particle' in order to combine the atoms. You'll see that they are now represented as a single sphere:
You can also break a particle by selecting it and pressing 'Suspend Particle' afterwards, to restore the underlying atoms. Or use the 'Extend / Reduce Members' option to temporarily break a selected particle and change the effected atoms.
Access this option by pressing 'Edit Identifiers' on a highlighted particle / atom. You will now be able to define the following fields:
Particle ID: Used to classify the particle. This identifier will only be used inside the MembraneEditor and is only relevant if you want to use the Atom Level Minimizer or future custom membrane algorithms that need access to this field. You can use the same identifier for multiple particles if you want them to be treated the same way. This may be important if a membrane algorithm uses this identifier to access specific force-field parameters.
You can also use a regular element-symbol if you want a particle to be treated as a usual atom later on.
Atom Name: This identifier will be used to define the field "Name" of the referring ATOM-entry in the final pdb file
Element: Will be used as the element-symbol in the final pdb file.
The button on the right side allows you to define a color for your particle. Particles with the same Particle ID will always get the same color.
It may be useful to wrap a single atom into a particle if you want to "overwrite" the identifiers, e.g. for a special treatment by a force field
Here's an example of a fully coarse-grained lipid. The different colors represent the different Particle ID's
- Written by bjoern
- Category: Cm2help 7. Atomic Representation
- Published: 14 September 2013
- Hits: 2111