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| 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:
ATOMS is present, then take the ordered list of atoms from the ATOMS keyword as a starting list.NDX_FILE is present, then append to it the list obtained from the gromacs group.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.SORT is present, then the resulting list is sorted by increasing serial number.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.
| 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 |
| 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 |
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'):
o: GROUP ATOMS=1,4,7,11,14 h: GROUP ATOMS=2,3,5,6,8,9,12,13 # compute the coordination among the two groups c: COORDINATION GROUPA=o GROUPB=h R_0=0.3 # 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=c FILE=colvar
Groups can be conveniently stored in a separate file. E.g. one could create a file named groups.dat which reads
#SETTINGS FILENAME=groups.dat # this is groups.dat o: GROUP ATOMS=1,4,7,11,14 h: GROUP ATOMS=2,3,5,6,8,9,12,13
and then include it in the main 'plumed.dat' file
INCLUDE FILE=groups.dat # compute the coordination among the two groups c: COORDINATION GROUPA=o GROUPB=h R_0=0.3 # print the coordination on file 'colvar' PRINT ARG=c FILE=colvar
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
# import group named 'Protein' from file index.ndx pro: GROUP NDX_FILE=index.ndx NDX_GROUP=Protein # dump all the atoms of the protein on a trajectory file DUMPATOMS ATOMS=pro FILE=traj.gro
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
# take one atom every three, that is oxygens ox: GROUP ATOMS=1-90:3 # take the remaining atoms, that is hydrogens hy: GROUP ATOMS=1-90 REMOVE=ox DUMPATOMS ATOMS=ox FILE=ox.gro DUMPATOMS ATOMS=hy FILE=hy.gro
1.8.14