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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.

Creating Particles

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.

Entering Identifiers

Access this option by pressing 'Edit Identifiers' on a highlighted particle / atom. You will now be able to define the following fields: 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
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