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 two 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

contract shortcuts

a: FIXEDATOM 
AT
compulsory keyword 
coordinates of the virtual atom 
=0,0,0 The FIXEDATOM action with label a calculates the following quantities:

 Quantity   
 Description  
a.x
the x coordinate of the virtual atom
a.y
the y coordinate of the virtual atom
a.z
the z coordinate of the virtual atom
a.mass
the mass of the virtual atom
a.charge
the charge of the virtual atom


b: FIXEDATOM 
AT
compulsory keyword 
coordinates of the virtual atom 
=0,0,1 The FIXEDATOM action with label b calculates the following quantities:

 Quantity   
 Description  
b.x
the x coordinate of the virtual atom
b.y
the y coordinate of the virtual atom
b.z
the z coordinate of the virtual atom
b.mass
the mass of the virtual atom
b.charge
the charge of the virtual atom


an: ANGLE 
ATOMS
the list of atoms involved in this collective variable (either 3 or 4 atoms). 
=a,b,15,20 The ANGLE action with label an calculates a single scalar value
RESTRAINT 
ARG
the arguments on which the bias is acting. 
=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 RESTRAINT action with label 

a: FIXEDATOM 
AT
compulsory keyword 
coordinates of the virtual atom 
=0,0,0 The FIXEDATOM action with label a calculates the following quantities:

 Quantity   
 Description  
a.x
the x coordinate of the virtual atom
a.y
the y coordinate of the virtual atom
a.z
the z coordinate of the virtual atom
a.mass
the mass of the virtual atom
a.charge
the charge of the virtual atom


b: FIXEDATOM 
AT
compulsory keyword 
coordinates of the virtual atom 
=0,0,1 The FIXEDATOM action with label b calculates the following quantities:

 Quantity   
 Description  
b.x
the x coordinate of the virtual atom
b.y
the y coordinate of the virtual atom
b.z
the z coordinate of the virtual atom
b.mass
the mass of the virtual atom
b.charge
the charge of the virtual atom


an: ANGLE 
ATOMS
the list of atoms involved in this collective variable (either 3 or 4 atoms). 
=a,b,15,20 The ANGLE action with label an calculates a single scalar value
@4: RESTRAINT_SCALAR 
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 RESTRAINT_SCALAR action with label @4 calculates the following quantities:

 Quantity   
 Description  
@4.bias
the instantaneous value of the bias potential
@4.force2
the instantaneous value of the squared force due to this bias potential

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

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 The FIT_TO_TEMPLATE action with label 
a: FIXEDATOM 
AT
compulsory keyword 
coordinates of the virtual atom 
=10,20,30 The FIXEDATOM action with label a calculates the following quantities:

 Quantity   
 Description  
a.x
the x coordinate of the virtual atom
a.y
the y coordinate of the virtual atom
a.z
the z coordinate of the virtual atom
a.mass
the mass of the virtual atom
a.charge
the charge of the virtual atom


d: DISTANCE 
ATOMS
the pair of atom that we are calculating the distance between. 
=a,20 The DISTANCE action with label d calculates a single scalar value
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 PRINT action with label 

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

Description of components

Quantity	Description
x	the x coordinate of the virtual atom
y	the y coordinate of the virtual atom
z	the z coordinate of the virtual atom
mass	the mass of the virtual atom
charge	the charge of the virtual atom

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