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Subset selection

This kind of selection is used when one wants to narrow an analysis on a given subset of atoms of the system. For instance, assuming that you performed a MD of a protein in a water box and that you are interested in calculating the diffusion constant of the protein via a Mean-Square Displacement (MSD) analysis. In that case, it will be necessary to perform the analysis only on the atoms of the protein. By default, nMOLDYN consider all the atoms for an analysis. The dialog from which a subset selection is performed is displayed in figure 4.19.

Figure 4.19: The dialog from where a subset selection is performed.

At the bottom of the dialog, the Actions frame contains the Cancel button to cancel the selection and the OK button to validate the selecton.

On the top of the dialog, three radiobuttons allows to select from which media the selection will be performed. This can be:

- from a selection file: this will perform the selection from a nMOLDYN subset selection file,
- from the loaded trajectory: this will perform the selection directly from the contents of the universe contained in the loaded trajectory,
- from an expression string: this will perform the selection from a valid python expression declaring a list of atoms to include in the selection.

When clicking on one of these radiobutton, a media-specific dialog will be displayed in the underneath frame.

Subsections

- selection from a selection file
- selection from the loaded trajectory
- selection from an expression string

Next: selection from a selection Up: Atom selection Previous: Atom selection Contents