Action: FIXEDATOM

Module	vatom
Description	Usage
Add a virtual atom in a fixed position.

Details and examples

Add a virtual atom in a fixed position.

This action creates a virtual atom at a fixed position. The example input below illustrates how this idea can be used to compute the angle between the vector connecting atoms 15 and 20 and the z axis and how this quantity can then be restrained so that the angle stays close to zero.

Click on the labels of the actions for more information on what each action computes

aThe FIXEDATOM action with label a calculates the following quantities: Quantity    Type    Description  
a atoms virtual atom calculated by FIXEDATOM action: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=0,0,0
a: FIXEDATOMAdd a virtual atom in a fixed position. This action uses the defaults shown here. More details ATcoordinates of the virtual atom=0,0,0  SET_MASS mass of the virtual atom=1 SET_CHARGE charge of the virtual atom=0
bThe FIXEDATOM action with label b calculates the following quantities: Quantity    Type    Description  
b atoms virtual atom calculated by FIXEDATOM action: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=0,0,1
b: FIXEDATOMAdd a virtual atom in a fixed position. This action uses the defaults shown here. More details ATcoordinates of the virtual atom=0,0,1  SET_MASS mass of the virtual atom=1 SET_CHARGE charge of the virtual atom=0
anThe ANGLE action with label an calculates the following quantities: Quantity    Type    Description  
an scalar the ANGLE involving these atoms: ANGLECalculate one or multiple angle/s. More details ATOMSthe list of atoms involved in this collective variable (either 3 or 4 atoms)=a,b,15,20
RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=an ATthe position of the restraint=0.0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=100.0

By default PLUMED assumes that any coordinates specified using the AT keyword specified are the cartesian coordinates of the fixed atom. However, if you use the SCALED_COMPONENTS flag as shown below:

Click on the labels of the actions for more information on what each action computes

aThe FIXEDATOM action with label a calculates the following quantities: Quantity    Type    Description  
a atoms virtual atom calculated by FIXEDATOM action: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=0.25,0.25,0.25 SCALED_COMPONENTS use scaled components
a: FIXEDATOMAdd a virtual atom in a fixed position. This action uses the defaults shown here. More details ATcoordinates of the virtual atom=0.25,0.25,0.25 SCALED_COMPONENTS use scaled components  SET_MASS mass of the virtual atom=1 SET_CHARGE charge of the virtual atom=0
DUMPATOMSDump selected atoms on a file. More details ATOMSthe atom indices whose positions you would like to print out=a FILEfile on which to output coordinates; extension is automatically detected=vatom.xyz

the coordinates specified using the AT keyword are interpretted as scaled coordinates. The positions output to the vatom.xyz file in the input above is thus obtained by multiplying the input vector by the cell vectors on every step. The position of the atom a thus changes as the box size changes.

It is also possible to assign a predefined charge or mass to the atom by using the SET_MASS and SET_CHARGE keywords.

This action, like POSITION is not invariant for translation of the system so adding a force on it can cause trouble.

The problem is that the vector connecting any atom and a virtual atom created using the FIXEDATOM atoms command is not invariant to translation. However, if, as has been done in the following example input, one first aligns atoms to a reference using FIT_TO_TEMPLATE, then it is safe to add further fixed atoms without breaking translational invariance.

Click on the labels of the actions for more information on what each action computes

#SETTINGS INPUTFILES=regtest/basic/rt63/align.pdb
FIT_TO_TEMPLATEThis action is used to align a molecule to a template. More details STRIDE the frequency with which molecules are reassembled=1 REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=regtest/basic/rt63/align.pdb Click here to see an extract from this file.
    ×  FILE: regtest/basic/rt63/align.pdb
    ATOM      1 HH31 ACE     1      -0.000  -0.000  00.000  1.00  0.00            
ATOM      2 HH31 ACE     1      -0.000  -0.000  00.000  0.50  0.00            
END
  
 TYPE the manner in which RMSD alignment is performed=SIMPLE
The FIT_TO_TEMPLATE action with label  calculates somethingaThe FIXEDATOM action with label a calculates the following quantities: Quantity    Type    Description  
a atoms virtual atom calculated by FIXEDATOM action: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=10,20,30
a: FIXEDATOMAdd a virtual atom in a fixed position. This action uses the defaults shown here. More details ATcoordinates of the virtual atom=10,20,30  SET_MASS mass of the virtual atom=1 SET_CHARGE charge of the virtual atom=0
dThe DISTANCE action with label d calculates the following quantities: Quantity    Type    Description  
d scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=a,20
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d FILEthe name of the file on which to output these quantities=colvar

Full list of keywords

The following table describes the keywords and options that can be used with this action

Keyword	Type	Default	Description
AT	compulsory	none	coordinates of the virtual atom
SET_MASS	compulsory	1	mass of the virtual atom
SET_CHARGE	compulsory	0	charge of the virtual atom
SCALED_COMPONENTS	optional	false	use scaled components

Quantity	Type	Description
a	atoms	virtual atom calculated by FIXEDATOM action