Manual

restraint

This option controls the applied motion restraint during molecular dynamics (MD) simulations.

`k`	The force constant in kcal/mol
	When it is greater than 0, it will restrain that two groups are closer than `d`
	When it is less than 0, it will restrain that two groups are farther than `d`
`d`	The distance threshold between the two groups of atoms in Angstrom
`atom_range1`	The first group of atoms to be restrained
`atom_range2`	The second group of atoms to be restrained

An example:

restraint
   dist 100 3.5 1-3 6 11 : 7-9 12 15-20
end

The potential is:

$U = \frac{1}{2} k (r_{12} - d)^{2}$

where $r_{1}$ and $r_{2}$ is the geometrical center of atom group 1 and 2, respectively.

This keyword adds position restraints for a group of atoms. The format is:

pos k file_name atom_range

`k`	The force constant in kcal/mol
`file_name`	The restrained positions for all atoms to be restrained in XYZ format (The element name does not matter)
`atom_range`	The group of atoms to be restrained
	The number of atoms in `atom_range` and `file_name` must be identical.

An example:

restraint
  pos 100. x-res.xyz  4-6 9
end

This means that atom 4,5,6,9 are to be restrained. The reference positions should be included in x-res.xyz:

4
reference positions
C 6.9731  -0.9546  7.5885
C 6.9902  -0.8940  7.3899
C 7.0270  -0.5192  7.3005
C 6.9631  -0.7656  7.4118

The potential is:

$U = \frac{1}{2} k (r - r_{0})^{2}$

where $r$ and $r_{0}$ is the real position and reference position of the atom, respectively.

This keyword restrains a group of atoms within a sphere. The format is:

sphere k d center_x center_y center_z atom_range

`k`	The force constant in kcal/mol
`d`	The radius of the restraining sphere in Angstrom
`center_x center_y center_z`	The center of the restraining sphere in Angstrom
`atom_range`	The atoms to be restrained

An example:

restraint
  sphere 10 10 0. 0. 0. 1 2 3-5 6-15
end

The potential is:

$U = \sum_{i}^{atom range} \frac{1}{2} k (r_{i c} - d)^{2}$

where $r_{i}$ is the position of atom $i$ , and $r_{c}$ is the center of the restraining sphere.

qmmm