Action: COM
| Module | vatom |
|---|---|
| Description | Usage |
| Calculate the center of mass for a group of atoms. |   |
| This action outputs data to a file. You can read more about how PLUMED manages output files here |
Input
The atoms that serve as the input for this action are specified using one or more of the keywords in the following table.
| Keyword | Type | Description |
|---|---|---|
| ATOMS | atoms | the list of atoms which are involved the virtual atom's definition |
Further details and examples
Calculate the center of mass for a group of atoms.
The following example input shows how you can use this shortcut to calculate the center of mass for atoms 1,2,3,4,5,6,7 and for atoms 15,20. You can then compute the distance between the two center of masses.
 |
c1: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1-7 c2: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=15,20 d1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c1,c2 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d1
The center of mass is stored as a virtual atom. As you can see from the above to refer to the position of the center of mass when specifying the atoms that should be used when calculating some other action you use the lable of the COM action that computes the center of mass of interest.
The COM command is a shortcut because it is a wrapper to CENTER. CENTER is more powerful than comm as it allows you to use arbitrary weights in place of the masses.
If you run with periodic boundary conditions these are taken into account automatically when computing the center of mass. The way this is handled is akin to the way molecules are rebuilt in the WHOLEMOLECULES command. However, at variance to WHOLEMOLECULES, the copies of the atomic positions in this action are modified. The global positions (i.e. those that are used in all other actions) are not changed when the alignment is performed.
If you believe that PBC should not be applied when calculating the position fo the center of mass you can use the NOPBC flag.
Syntax
The following table describes the keywords and options that can be used with this action
| Keyword | Type | Default | Description |
|---|---|---|---|
| ATOMS | input | none | the list of atoms which are involved the virtual atom's definition |
| WEIGHTS | optional | not used | Center is computed as a weighted average |
| SET_CHARGE | optional | not used | Set the charge of the virtual atom to a given value |
| SET_MASS | optional | not used | Set the mass of the virtual atom to a given value |
| NOPBC | optional | false | ignore the periodic boundary conditions when calculating distances |
| MASS | optional | false | If set center is mass weighted |
| PHASES | optional | false | Compute center using trigonometric phases |