5.3 Atom constraints OpenGL

With VEGA 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:

Constraint options

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 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.