FIXEDATOM
This is part of the vatom module

Add a virtual atom in a fixed position.

This action creates a virtual atom at a fixed position. The coordinates can be specified in Cartesian components (by default) or in scaled coordinates (SCALED_COMPONENTS). It is also possible to assign a predefined charge or mass to the atom.

Attention
Similar to POSITION this variable is not invariant for translation of the system. Adding a force on it can create serious troubles.

Notice that the distance between to atoms created using FIXEDATOM is invariant for translation. Additionally, if one first align atoms to a reference using FIT_TO_TEMPLATE, then it is safe to add further fixed atoms without breaking translational invariance.

Examples

The following input instructs plumed to compute the angle between distance of atoms 15 and 20 and the z axis and keeping it close to zero.

Click on the labels of the actions for more information on what each action computes
tested on master
a: FIXEDATOM 
AT
compulsory keyword coordinates of the virtual atom
=0,0,0 b: FIXEDATOM
AT
compulsory keyword coordinates of the virtual atom
=0,0,1 an: ANGLE
ATOMS
the list of atoms involved in this collective variable (either 3 or 4 atoms).
=a,b,15,20 RESTRAINT
ARG
the input for this action is the scalar output from one or more other actions.
=an
AT
compulsory keyword the position of the restraint
=0.0
KAPPA
compulsory keyword ( default=0.0 ) specifies that the restraint is harmonic and what the values of the force constants on each of the variables are
=100.0

The following input instructs plumed to align a protein to a template and to then compute the distance between one of the atoms in the protein and the point (10,20,30).

Click on the labels of the actions for more information on what each action computes
tested on master
FIT_TO_TEMPLATE 
STRIDE
compulsory keyword ( default=1 ) the frequency with which molecules are reassembled.
=1
REFERENCE
compulsory keyword a file in pdb format containing the reference structure and the atoms involved in the CV.
=ref.pdb
TYPE
compulsory keyword ( default=SIMPLE ) the manner in which RMSD alignment is performed.
=SIMPLE a: FIXEDATOM
AT
compulsory keyword coordinates of the virtual atom
=10,20,30 d: DISTANCE
ATOMS
the pair of atom that we are calculating the distance between.
=a,20 PRINT
ARG
the input for this action is the scalar output from one or more other actions.
=d
FILE
the name of the file on which to output these quantities
=colvar

The reference structure to align to is provided in a pdb file called ref.pdb as shown below:

ATOM      8  HT3 ALA     2      -1.480  -1.560   1.212  1.00  1.00      DIA  H
ATOM      9  CAY ALA     2      -0.096   2.144  -0.669  1.00  1.00      DIA  C
ATOM     10  HY1 ALA     2       0.871   2.385  -0.588  1.00  1.00      DIA  H
ATOM     12  HY3 ALA     2      -0.520   2.679  -1.400  1.00  1.00      DIA  H
ATOM     14  OY  ALA     2      -1.139   0.931  -0.973  1.00  1.00      DIA  O
END
Glossary of keywords and components
The atoms involved can be specified using
ATOMS the list of atoms which are involved the virtual atom's definition. For more information on how to specify lists of atoms see Groups and Virtual Atoms
Compulsory keywords
AT coordinates of the virtual atom
SET_MASS ( default=1 ) mass of the virtual atom
SET_CHARGE ( default=0 ) charge of the virtual atom
Options
SCALED_COMPONENTS

( default=off ) use scaled components