 | |
| | | Command | | Argument |
| Datatype | | Default | | Min | | Max |
| | | Format: | | Fix<Atom|Res|Mol|Obj|All> |
| Selection | | SELECTION |
| - |
| - | | - | |
| | Python: | | Fix<Atom|Res|Mol|Obj|All>(selection1) |
| | | Menu: | | Simulation > Fix | | |
| Related: |
| Free
| | | |
| Required: | |  | |
|
The Fix
command makes sure that the selected atoms do not move during a simulation or Experiment. To indicate the fixed state, the atoms are additionally
colored yellow. Fixing can be reversed with the Free
command.
- When the NOVA force field is used and at least one atom in a planar group is fixed, YASARA fixes also all the other atoms in the group to avoid numerical instabilities in the way NOVA treats planarity.
- When a molecule is partly outside the non-periodic cell, atoms close to the cell wall are fixed automatically to avoid geometry distortions caused by the repulsive cell wall forces.
Example:
FixAtom Backbone
Fix all backbone atoms during a simulation.
Example macro:
# EXAMPLE Fix
# Requires YASARA Dynamics
Clear
LoadPDB 1crn
Clean
FixAtom Backbone
StickAtom Sidechain
Sim On
Wait 20
 | | Figure: Result of the example macro above. |
| 
