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Atom selection

It is sometimes necessary to define a subset of atoms on which a given action or analysis will be performed. nMOLDYN provided this possibility by a general mechanism that can be applied to several selection types such as:

- Subset selection: selection of a subset of atoms on which an analysis will be performed,
- Deuteration selection: definition of a subset of hydrogen atoms whose parameters will be the ones of deuterium. This allows to account for isotopic deuteration replacement performed in neutron experiments,
- Group selection: definition of one or several groups of atoms on which a given action will be performed collectively.

Albeit different in their nature, we will see in the following sections, that all these selections use the same syntax what is quite convenient from a user point of view.

Subsections

- Subset selection
  - selection from a selection file
  - selection from the loaded trajectory
  - selection from an expression string
- Deuteration selection
  - selection from a selection file
  - selection from the loaded trajectory
  - selection from an expression string
- Group selection
  - selection from a selection file
  - selection from the loaded trajectory
  - selection from an expression string