6.3 Atom constraints
With VEGA ZZ it's possible specify a constraint constant for each atom in order to fix/constraint them in molecular dynamics simulations (e.g. NAMD). The dialog box is accessible trough the Edit -> Coordinates -> Constraints menu item:
The user can choose the Fix/Free mode for atom fixing/freeing or the Value mode for harmonic constraints (see the manual of the molecular dynamics software). In the Value field of the Parameters box, one can put the harmonic constant that can be from 0 (full free) to 1 (full fix). In the Selection box, one can select the atoms to apply the constraints. The Visible atoms options should be used with the Atom selection dialog box for complex constraints applications. Checking Color atoms, the atoms are colored by constraint value (blue = fix, green = free) as shown in the Colors box.
Examples:
![]() |
Fixed backbone |
Freed a sphere around an atom | ![]() |
WARNING:
Please remember that the only two file formats can store the atom constraints
and they are the IFF and the PDB. VEGA ZZ can read the constraints only from IFF
files and it can write in both formats. In PDB files the constraints are placed
in the B column and it's possible only if the File -> Constraints item
is checked in the main menu.