6.3 Atom constraints

VEGA ZZ allows to specify constraint constants for each atom in order to fix/constraint them in molecular dynamics simulations (e.g. NAMD). The dialog box is accessible by Edit Coordinates Constraints menu item:


Constraint options


You can choose Fix/Free mode to fix/free atoms or Value mode for harmonic constraints (see the manual of the molecular dynamics software). In Value field of Parameters box, you can put the harmonic constant that can be from 0 (full free) to 1 (full fix). In Selection box, you can select the atoms to apply the constraints. Visible atoms options should be used with  Atom selection dialog box for complex constraints. Checking Color atoms, the atoms are colored by constraint value (blue = fix, green = free) as shown in the Colors box.



Fixed backbone    Fixed backbone
Freed a sphere around an atom    Sphere around an atom


Remember that two file formats only can store the atom constraints and they are IFF and PDB. VEGA ZZ can read the constraints only from IFF files and it can write them to both formats. In PDB files, the constraints are placed in B column.