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# Pulling and stepping mode

This feature can be used to mimic force atomic microscopy experiments (pulling mode) as described in Ref. [24,27]. In such computer experiments enzyme-ligand binding can be investigated by exerting a pulling force to the ligand while the center of mass of the enzyme is held fixed by a harmonic potential. If the pulling force is strong enough and points in the direction the enzyme-ligand complex will rupture.

There are two different modes, namely mode `1' (or `4') and mode `2' (or `5'), to manage pulling in EGO. If one enters `1' or `4' for the pulling mode a `virtual' harmonic spring is used to excert a pulling force as described in [24,27]. In that mode, one has to specify the atom to which one of the ends of the artifical spring is connected to. Note: Only one atom must be selected in the subsequent selection string! Furthermore, one has to specify the movement of the other end of the spring, i.e., one has to enter the speed (given in Å/ps) and the direction of movement into the following two lines. At least, one has to specify the spring constant, i.e., the spring constant acting parallel to the pulling direction and the spring constant perpendicular to the pulling direction. Usually the spring constant perpendicular to the pulling direction is set to zero.

The modes `1' or `4' differ only in the way how the pulling direction is defined. If one chooses mode `1' the pulling direction is given as a vector with carthesian coordinates. If one chooses mode `2' the pulling direction is defined by the interconection line of two atoms. That direction is determined from the positions of the two atoms at the start of EGO and will not change during a simulation even if the positions of the two atoms will change.
Example 1: (To atom 3 a `spring' is attached pulling to the positive x direction)
1 Pulling mode (0=OFF,1=Pulling,2=Stepping). Next line is atom sel. string:
A3
10.0 Speed of pulling in A/ps.
1.000000 0.000000 0.000000 Pulling direction (dx,dy,dz).
20.00000 0.000000 Spring-constants (||,T) in kcal/(mol A).

Example 2:(To atom 3 a `spring' is attached pulling to the direction defined by the interconection line of atom 5 and 8.)
4 Pulling mode (0=OFF,1=Pulling,2=Stepping). Next line is atom sel. string:
A3
10.0 Speed of pulling in A/ps.
5 8 Pulling direction (dx,dy,dz).
20.00000 0.000000 Spring-constants (||,T) in kcal/(mol A).

Corresponding to the two pulling modes there are also two `stepping' modes (mode `2' or `5'). With `stepping' one can move an atom or a group of atoms with a given velocity in a certain direction. Consequently, in that mode the selection string may define a set of atoms (e.g., a methyl-group). Any internal dynamics of such a selected group of atoms is frozen. The values set for the spring constant are meaningless in that modes.

Next: The Free Format Section Up: The Control File Previous: Switch for using immobilisation
Helmut Heller
2000-04-19