Qmmm preparation constraints

Fixing atoms outside a certain distance from the QM region can also be accomplished using prepare module. These constraints will then be permanently embedded in the resulting restart file, which may be advantageous for certain types of QM/MM simulations. The actual format for the constraint directive to fix whole residues is

fix segments beyond  <real radius>  <integer residue number>:<string atom name>

or to fix on atom basis

fix atoms beyond  <real radius>  <integer residue number>:<string atom name>

This example illustrates the use of permanent fix directives during preparation stage

start etl
source etl0.pdb
new_top new_seq
#solvation in 40 A cubic box
solvate cube 4.0
modify segment 1 quantum
#fix residues more than 20 A away from ethanol oxygen atom
fix segments beyond 2.0 1:_O
update lists
write etl_ref.rst
write etl_ref.pdb
task prepare