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SHAKE is a method of fixing bond lengths and, optionally, bond
angles during dynamics. The method was brought to CHARMM by Wilfred Van
Gunsteren, and is referenced in J. Comp. Phys. 23, 327 (1977).
When hydrogens are present in a structure, it will allow a five fold
increase in the step size if SHAKE is used on the bonds.
To use SHAKE, one specifies the SHAKE command
before any dynamics are run. The SHAKE command has the following
syntax:
SHAKE [ BONH [ BOND [ ANGH [ ANGL ]]]]
BONH specifies that all bonds involving hydrogens are to be fixed. BOND specifies all bonds. ANGH specifies that all angles involving hydrogen must be fixed. ANGL specifies that all angles must be shaken. BOND must be specified if angles are fixed.
When the SHAKE command is used, it will check that there
are degrees of freedom available for all atoms to satisfy all their
constraints. Angles cannot be fixed with SHAKE if one has
explicit hydrogen arginines in the structure as the CZ carbon has too
many constraints. This is a general problem for any structure which has
too many branches close together.
SHAKE is not recommended for fixing angles. The algorithm
converges very slowly in the case where one has three angles centered on
a tetravalent atom and the constraints are satisfiable only using out of
plane motions.
The use of SHAKE modifies the output of the dynamics
command. The number appearing to the right of the step number is the
number of iterations SHAKE required to satisfy all the
constraints. This number should generally be small.
If atoms are fixed rigidly in place, see Fixed Atoms, then the SHAKE command should follow the CONS command for to prevent SHAKE from shaking deleted bonds. This will make it run more efficiently.
Each time the SHAKE command is executed, the list of constraints is initialized. Thus, if you wish to eliminate the use of SHAKE, specify a SHAKE command with no arguments.