Symmetry Restraints

Symmetry restraints are based on symmetrical relationships between monomers. Defined monomers are transformed to overlap and an average position for each atom is calculated. After the average structure is transformed back, a harmonic force is calculated which drives each monomer to the average.

• symmetryRestraints $<$ Are symmetry restraints active? $>$
  Acceptable Values: on or off
  Default Value: off
  Description: Should Symmetry constraining forces be applied to the system. If symmetry restraints are enabled, symmetryk* and symmetryFile must be defined in the input file as well. *See symmetryk entry for details.

• symmetryFirstFullStep $<$ First step to apply full harmonic force $>$
  Acceptable Values: Non-negative integer
  Default Value: symmetryFirstStep
  Description: Force constant symmetryk linearly increased from symmetryFirstStep to symmetryFirstFullStep

• symmetryLastFullStep $<$ Last step to apply full harmonic force $>$
  Acceptable Values: Non-negative integer
  Default Value: symmetryLastStep
  Description: Force constant symmetryk linearly decreased from symmetryLastFullStep to symmetryLastStep

• symmetryk $<$ Constant for harmonic restraining forces $>$
  Acceptable Values: Positive value
  Description: Harmonic force constant. Scaled down by number of atoms in the monomer. If this setting is omitted, the value in the occupancy column of the pdb file specified by symmetrykFile will be used as the constant for that atom. This allows the user to specify the constant on a per-atom basis.

• symmetrykFile $<$ pdb containing per atom force constants $>$
  Acceptable Values: Path to pdb file
  Description: pdb where the occupancy column specifies the per atom force constants. If using overlapping symmetry groups, you must include one additional symmetrykfile per symmetryFile

• symmetryScaleForces $<$ Scale symmetry restraints over time $>$
  Acceptable Values: on or off
  Default Value: off
  Description: If turned on, the harmonic force applied by the symmetry restraints will linearly evolve with each time step based on symmetryFirstFullStep and symmetryLastFullStep.

• symmetryFile $<$ File for symmetry information $>$
  Acceptable Values: Path to PDB file
  Description: Restrained atoms are those whose occupancy (O) is nonzero in the symmetry pdb file. The file must contain no more atoms than the structure file and those atoms present must have the exact same index as the structure file (i.e., the file may contain a truncated atom selection ``index $< N$ '' but not an arbitrary selection). The value in the occupancy column represent the "symmetry group" the atom belongs to. These symmetry groups are used for denoting monomers of the same type. These groups will be transformed by the matrices in their own symmetryMatrixFile and averaged separetely from other groups. The designation in the occupancy column should be an integer value starting at 1 and proceeding in ascending order, mirroring the order of the corresponding matrix file within the configuration file (e.g. the first symmetryMatrixFile contains the matrices for symmetry group 1). The value in the atom's beta column represents its monomer designation. This should be an integer value starting at 1 and proceeding in ascending order, relative to the order of the corresponding transformation matrix found in the symmetry group's symmetryMatrixFile. If an atom is contained in more than one symmetry group, additional pdb files can be listed. These pdb files should follow the same rules as the first one (unique group and monomer identifiers in increasing order).

• symmetryMatrixFile $<$ File for transformation matrices $>$
  Acceptable Values: Path to matrix file
  Description: The symmetryMatrixFile is a path to a file that contains a list of transformation matrices to make the monomers overlap. The file should contain one (and only one) matrix for each monomer in the order of monomer ID designated in the symmetryFile. Each symmetry group should have its own symmetryMatrixFile file containing only the matrices used by the monomers in that group. These should be formatted with spaces between columns and NO spaces between rows as follows:

  1 0 0 0
  0 1 0 0
  0 0 1 0
  0 0 0 1
  

  with different matrices separated by a single blank line (and no line before the first or after the last matrix). This file is OPTIONAL. Leave this line out to have namd generate the transformations for you.

• symmetryFirstStep $<$ first symmetry restraint timestep $>$
  Acceptable Values: Non-negative integer
  Default Value: 0
  Description:
• symmetryLastStep $<$ last symmetry restraint timestep $>$
  Acceptable Values: Positive integer
  Default Value: infinity
  Description: Symmetry restraints are applied only between symmetryFirstStep and symmetryLastStep. Use these settings with caution and ensure restraints are only being applied when necessary (e.g. not during equilibration).