GROUP

This is part of the generic module

Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms.

Atoms can be listed as comma separated numbers (i.e. 1,2,3,10,45,7,9) , simple positive ranges (i.e. 20-40), ranges with a stride either positive or negative (i.e. 20-40:2 or 80-50:-2) or as comma separated combinations of all the former methods (1,2,4,5,10-20,21-40:2,80-50:-2).

Moreover, lists can be imported from ndx files (GROMACS format). Use NDX_FILE to set the name of the index file and NDX_GROUP to set the name of the group to be imported (default is first one).

It is also possible to remove atoms from a list and or sort them using keywords REMOVE, SORT, and UNIQUE. The flow is the following:

• If ATOMS is present, then take the ordered list of atoms from the ATOMS keyword as a starting list.
• If NDX_FILE is present, then append to it the list obtained from the gromacs group.
• If REMOVE is present, then remove the first occurrence of each of these atoms from the list. If one tries to remove an atom that was not listed plumed adds a notice in the output. An atom that is present twice in the original list might be removed twice.
• If SORT is present, then the resulting list is sorted by increasing serial number.
• If UNIQUE is present, then the resulting list is sorted by increasing serial number and duplicate elements are removed.

Notice that this command just creates a shortcut, and does not imply any real calculation. So, having a huge group defined does not slow down your calculation in any way. It is just convenient to better organize input files. Might be used in combination with the INCLUDE command so as to store long group definitions in a separate file.

Examples

This command create a group of atoms containing atoms 1, 4, 7, 11 and 14 (labeled 'o'), and another containing atoms 2, 3, 5, 6, 8, 9, 12, and 13 (labeled 'h'):

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

o: GROUP 
ATOMS
the numerical indexes for the set of atoms in the group. 
=1,4,7,11,14 The GROUP action with label o defines a group of atoms so that they can be referred to later in the input
h: GROUP 
ATOMS
the numerical indexes for the set of atoms in the group. 
=2,3,5,6,8,9,12,13 The GROUP action with label h defines a group of atoms so that they can be referred to later in the input
# compute the coordination among the two groups
c: COORDINATION 
GROUPA
First list of atoms. 
=o 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted). 
=h 
R_0
 could not find this keyword 
=0.3 The COORDINATION action with label c calculates a single scalar value
# same could have been obtained without GROUP, just writing:
# c: COORDINATION GROUPA=1,4,7,11,14 GROUPB=2,3,5,6,8,9,12,13
# print the coordination on file 'colvar'
PRINT 
ARG
the input for this action is the scalar output from one or more other actions. 
=c 
FILE
the name of the file on which to output these quantities 
=colvar The PRINT action with label 

Groups can be conveniently stored in a separate file. E.g. one could create a file named groups.dat which reads

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

#SETTINGS FILENAME=groups.dat
# this is groups.dat
o: GROUP 
ATOMS
the numerical indexes for the set of atoms in the group. 
=1,4,7,11,14 The GROUP action with label o defines a group of atoms so that they can be referred to later in the input
h: GROUP 
ATOMS
the numerical indexes for the set of atoms in the group. 
=2,3,5,6,8,9,12,13 The GROUP action with label h defines a group of atoms so that they can be referred to later in the input

and then include it in the main 'plumed.dat' file

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

INCLUDE 
FILE
compulsory keyword 
file to be included 
=groups.dat The INCLUDE action with label 
# compute the coordination among the two groups
c: COORDINATION 
GROUPA
First list of atoms. 
=o 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted). 
=h 
R_0
 could not find this keyword 
=0.3 The COORDINATION action with label c calculates a single scalar value
# print the coordination on file 'colvar'
PRINT 
ARG
the input for this action is the scalar output from one or more other actions. 
=c 
FILE
the name of the file on which to output these quantities 
=colvar The PRINT action with label 

The groups.dat file could be very long and include lists of thousand atoms without cluttering the main plumed.dat file.

A GROMACS index file such as the one shown below:

[ Protein ]
1 3 5 7 9
2 4 6 8 10
[ Group2 ]
30 31 32 33 34 35 36 37 38 39 40
5

can also be imported by using the GROUP keyword as shown below

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

# import group named 'Protein' from file index.ndx
pro: GROUP 
NDX_FILE
the name of index file (gromacs syntax) 
=index.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used
by default 
=Protein The GROUP action with label pro defines a group of atoms so that they can be referred to later in the input
# dump all the atoms of the protein on a trajectory file
DUMPATOMS 
ATOMS
the atom indices whose positions you would like to print out. 
=pro 
FILE
compulsory keyword 
file on which to output coordinates; extension is automatically detected 
=traj.gro The DUMPATOMS action with label 

A list can be edited with REMOVE. For instance, if you are using a water model with three atoms per molecule, you can easily construct the list of hydrogen atoms in this manner

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

# take one atom every three, that is oxygens
ox: GROUP 
ATOMS
the numerical indexes for the set of atoms in the group. 
=1-90:3 The GROUP action with label ox defines a group of atoms so that they can be referred to later in the input
# take the remaining atoms, that is hydrogens
hy: GROUP 
ATOMS
the numerical indexes for the set of atoms in the group. 
=1-90 
REMOVE
remove these atoms from the list. 
=ox The GROUP action with label hy defines a group of atoms so that they can be referred to later in the input
DUMPATOMS 
ATOMS
the atom indices whose positions you would like to print out. 
=ox 
FILE
compulsory keyword 
file on which to output coordinates; extension is automatically detected 
=ox.gro The DUMPATOMS action with label 
DUMPATOMS 
ATOMS
the atom indices whose positions you would like to print out. 
=hy 
FILE
compulsory keyword 
file on which to output coordinates; extension is automatically detected 
=hy.gro The DUMPATOMS action with label 

Glossary of keywords and components

The atoms involved can be specified using

ATOMS	the numerical indexes for the set of atoms in the group. For more information on how to specify lists of atoms see Groups and Virtual Atoms
REMOVE	remove these atoms from the list. For more information on how to specify lists of atoms see Groups and Virtual Atoms

Options

SORT	( default=off ) sort the resulting list
UNIQUE	( default=off ) sort atoms and remove duplicated ones
NDX_FILE	the name of index file (gromacs syntax)
NDX_GROUP	the name of the group to be imported (gromacs syntax) - first group found is used by default