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.

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

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.

a: FIXEDATOM AT=0,0,0
b: FIXEDATOM AT=0,0,1
an: ANGLE ATOMS=a,b,15,20
RESTRAINT ARG=an AT=0.0 KAPPA=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).

FIT_TO_TEMPLATE STRIDE=1 REFERENCE=ref.pdb TYPE=SIMPLE
a: FIXEDATOM AT=10,20,30
d: DISTANCE ATOMS=a,20
PRINT ARG=d FILE=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