Interface restraints

#===============================================================================
# Restraints example 1: restraints syntax
#===============================================================================

# Here, the restraints are used as a standalone iterface, although the most
# common application of this interface is to use it as a modifier added to
# some other calculation. The purpose of this example is to demonstrate the
# syntax used to define all types of the restraints.

# Using the retsraints, we define a simple harmonic forcefield for a hydrogen
# peroxide, and optimize a very bad starting geometry using this forfecield.

job: optimize
interface: restraints

# Geometry - practically random guess
geometry: |
  H  1.0 0.0 0.0
  O  0.0 1.0 0.0
  O  0.0 0.0 5.0
  H  1.0 0.0 8.0

# The list of the restraints is an array in the YAML syntax (indented lines
# starting with "-"). Each line contain multiple entries, separated by
# semicolons:
# 1)       type of the internal coordinate (distance, angle, torsion)
# 2)       equilibrium value (in Angstroms/degrees)
# 3)       force constant (kcal/mol/Angstrom, kcal/mol/rad)
# 4,5,...) list of atoms (in Cuby selection syntax) defining the center the 
#          restraint is applied to (2 for distance, 3 for angle, 4 for torsion)
restraints:
  - distance; 0.95; 10; 1; 2
  - distance; 1.47; 10; 2; 3
  - distance; 0.95; 10; 3; 4
  - angle; 94.8; 10; 1; 2; 3
  - angle; 94.8; 10; 2; 3; 4
  - torsion; 111.5; 10; 1; 2; 3; 4

#===============================================================================
# Restraints example 2: Restraint as a modifier, acting on more atoms
#===============================================================================

# Optimization of water dimer, with restraint on the distance between the
# molecules. When more atoms are used as the restraint centers, the additional
# potential acts on their center of mass.

job: optimize

interface: water_ff # Simple forcefield for water, built in in Cuby

geometry: S66:01 # Optimized water dimer from the S66 database

modifiers: restraints # This adds a modifier to the calculation specified above

# Each modifier has its own block (subsection) in the input, named
# modifier_[modifier_name]. The contents of a block are indented to distinguish
# it from the remainder of the input.

modifier_restraints:
  # The setup of the modifier comes here - a restraint is defined
  # The two molecules are defined by atom selections (using difefrent way for
  # each of them - "1-3" and "4,5,6")
  restraints:
    - distance; 5.0; 20.0; 1-3; 4,5,6

#===============================================================================
# Restraints example 3: Flat-bottom distance restraint
#===============================================================================

# Molecular dynamics of water dimer, the dimer is prevented from dissociating
# by applying a restraint that has a flat bottom but adds a harmotic potential
# above a thershold distance.

job: dynamics
# NVT at 1000K, at this temperature the dimer will dissociate quickly
# when the restraint is not applied
thermostat: berendsen
temperature: 1000 # target temperature for the thermostat, K
init_temp: 1000 # initialization temperature, K
maxcycles: 10000
trajectory_freq: 50

interface: water_ff # Simple forcefield for water, built in in Cuby

geometry: S66:01 # Optimized water dimer from the S66 database

modifiers: restraints # This adds a modifier to the calculation specified above

# Each modifier has its own block (subsection) in the input, named
# modifier_[modifier_name]. The contents of a block are indented to distinguish
# it from the remainder of the input.

modifier_restraints:
  # The setup of the modifier comes here - a restraint is defined
  # The third number (8.0) is the additional parameter, below this distance
  # no restraint is applied.
  restraints:
    - distance_f; 5.0; 20.0; 8.0; 1-3; 4-6

#===============================================================================
# Restraints example 4: Distance diference restraint
#===============================================================================

# Optimization of water dimer cation with a distance difefrence restraint that
# keeps it non-symmetric

# Optimization setup
job: optimize
opt_quality: 0.1

# QM calculation: HF/6-31G
interface: turbomole
method: hf
basisset: 6-31G
charge: 1


# Restraint modifier
modifiers: restraints
modifier_restraints:
  restraints:
    - distance_difference; 1.0; 500.0; 1; 3; 3; 5
# The restraint definition requires four atoms A; B; C; D
# The restraint is applied is applied on the distance difference |AB| - |CD|
# Difference of 1.0 A is enforced using force constant of 500 kcal/mol/A

# Geometry - rough estimate built from neutral water dimer
geometry: |
 O     2.220871     0.026717     0.000620
 H    -1.022193     0.846776    -0.011489
 H     0.257521     0.042122     0.005219
 H    -1.440667    -0.653463     0.026409
 O    -0.702196    -0.056060     0.009942
 H     2.597493    -0.411663     0.766745
 H     2.593136    -0.449496    -0.744782