Next: Calculation of the Hesse-Matrix Up: The Free Format Section Previous: Control of minimization

## Control of constraints

In the free format section there are three keywords (SHAKEOFF, FORCEOFF and SPEEDOFF) which control constraints.

The keyword SHAKEOFF is used to patch the list of hydrogen atoms with constraint bond length (SHAKE algorithm). Usually, if one sets TRUE in `Switch for SHAKE on Hydrogens' all hydrogen atoms are shaked (see Section 4.21). If however, one wants to deselect a set of hydrogen atoms which should not be shaked, one can use the command SHAKEOFF in the free format section.
Example:
SHAKEOFF A* -RTIP3
The selection string `A* -RTIP3' selects all atoms which do not belong to a TIP3 residue and, therefore, switches off the SHAKE algorithm for these atoms. Consequently, only TIP3 hydrogens are shaked (if, of course, TRUE is set in `Switch for SHAKE on Hydrogens').

The keywords FORCEOFF and SPEEDOFF can be used to switch off the forces and the velocity of a selected set of atoms. Consequently, the selected atoms will not move while all other atoms will move. Usually both keywords are used together each selecting the same set of atoms. As an example application of these keywords one may think of a protein-water system. Let us suppose that a non-optimal setup of that protein-water system has `produced' a lot of water molecules which have van der Waals overlaps with the protein. A minimization starting from such a structure will strongly affect the protein structure as the overlapping water molecules strongly repell the protein atoms. This can be avoided if one constraints the atom positions of the protein by selecting all protein atoms as given in the example below.
FORCEOFF A* -RTIP3
SPEEDOFF A* -RTIP3
Then only the water molecules can move and the protein structure will be unaffected.

Next: Calculation of the Hesse-Matrix Up: The Free Format Section Previous: Control of minimization
Helmut Heller
2000-04-19