Using Groups¶
(1)¶\[4\pi r^2 g_{AB}(r) ~=~ V~\sum_{i \in A}^{N_A} \sum_{j \in B}^{N_B} P(r)\]
By having the user define the atom numbers for groups A and B in a simple file, we can calculate this \(g_{AB}\) in the most general way, without having to make any assumptions in the RDF program about the type of particles.
Groups can therefore consist of a series of atom numbers, but in some
cases also of molecule numbers. It is also possible to specify a
series of angles by triples of atom numbers, dihedrals by
quadruples of atom numbers and bonds or vectors (in a molecule) by
pairs of atom numbers. When appropriate the type of index file will
be specified for the following analysis programs. To help creating such
index file index.ndx
), there are a couple of programs to generate
them, using either your input configuration or the topology. To generate
an index file consisting of a series of atom numbers (as in the
example of \(g_{AB}\)), use gmx make_ndx
or gmx select. To generate an index file with
angles or dihedrals, use gmx mk_angndx. Of course you can also
make them by hand. The general format is presented here:
[ Oxygen ]
1 4 7
[ Hydrogen ]
2 3 5 6
8 9
First, the group name is written between square brackets. The following atom numbers may be spread out over as many lines as you like. The atom numbering starts at 1.
Each tool that can use groups will offer the available alternatives for the user to choose. That choice can be made with the number of the group, or its name. In fact, the first few letters of the group name will suffice if that will distinguish the group from all others. There are ways to use Unix shell features to choose group names on the command line, rather than interactively. Consult our webpage for suggestions.
Default Groups¶
When no index file is supplied to analysis tools or grompp, a number of default groups are generated to choose from:
System
- all atoms in the system
Protein
- all protein atoms
Protein-H
- protein atoms excluding hydrogens
C-alpha
- C\(_{\alpha}\) atoms
Backbone
- protein backbone atoms; N, C\(_{\alpha}\) and C
MainChain
- protein main chain atoms: N, C\(_{\alpha}\), C and O, including oxygens in C-terminus
MainChain+Cb
- protein main chain atoms including C\(_{\beta}\)
MainChain+H
- protein main chain atoms including backbone amide hydrogens and hydrogens on the N-terminus
SideChain
- protein side chain atoms; that is all atoms except N, C\(_{\alpha}\), C, O, backbone amide hydrogens, oxygens in C-terminus and hydrogens on the N-terminus
SideChain-H
- protein side chain atoms excluding all hydrogens
Prot-Masses
- protein atoms excluding dummy masses (as used in virtual site constructions of NH\(_3\) groups and tryptophan side-chains), see also sec. Virtual sites; this group is only included when it differs from the
Protein
group Non-Protein
- all non-protein atoms
DNA
- all DNA atoms
RNA
- all RNA atoms
Water
- water molecules (names like
SOL
,WAT
,HOH
, etc.) Seeresiduetypes.dat
for a full listing non-Water
- anything not covered by the
Water
group Ion
- any name matching an Ion entry in
residuetypes.dat
Water_and_Ions
- combination of the
Water
andIons
groups molecule_name
- for all residues/molecules which are not recognized as protein, DNA, or RNA; one group per residue/molecule name is generated
Other
- all atoms which are neither protein, DNA, nor RNA.
Empty groups will not be generated. Most of the groups only contain
protein atoms. An atom is considered a protein atom if its residue name
is listed in the
residuetypes.dat
file and is listed as a “Protein” entry. The process for determinding
DNA, RNA, etc. is analogous. If you need to modify these
classifications, then you can copy the file from the library directory
into your working directory and edit the local copy.
Selections¶
- The selections are specified as text instead of reading fixed atom indices from a file, using a syntax similar to VMD. The text can be entered interactively, provided on the command line, or from a file.
- The selections are not restricted to atoms, but can also specify that the analysis is to be performed on, e.g., center-of-mass positions of a group of atoms. Some tools may not support selections that do not evaluate to single atoms, e.g., if they require information that is available only for single atoms, like atom names or types.
- The selections can be dynamic, i.e., evaluate to different atoms for different trajectory frames. This allows analyzing only a subset of the system that satisfies some geometric criteria.
As an example of a simple selection, resname ABC
and
within 2 of resname DEF
selects all atoms in residues named ABC that are
within 2nm of any atom in a residue named DEF.
Tools that accept selections can also use traditional index files similarly to older tools: it is possible to give an ndx file to the tool, and directly select a group from the index file as a selection, either by group number or by group name. The index groups can also be used as a part of a more complicated selection.
To get started, you can run gmx select with a single
structure, and use the interactive prompt to try out different
selections. The tool provides, among others, output options
-on
and -ofpdb
to write out the selected
atoms to an index file and to a pdb file, respectively.
This does not allow testing selections that evaluate to center-of-mass
positions, but other selections can be tested and the result examined.
The detailed syntax and the individual keywords that can be used in
selections can be accessed by typing help
in the
interactive prompt of any selection-enabled tool, as well as with
gmx help selections. The help is divided into subtopics
that can be accessed with, e.g., help syntax
/
gmx help selections syntax
. Some individual selection
keywords have extended help as well, which can be accessed with, e.g.,
help keywords
within.
The interactive prompt does not currently provide much editing
capabilities. If you need them, you can run the program under
rlwrap
.
For tools that do not yet support the selection syntax, you can use gmx select -on to generate static index groups to pass to the tool. However, this only allows for a small subset (only the first bullet from the above list) of the flexibility that fully selection-aware tools offer.
It is also possible to write your own analysis tools to take advantage
of the flexibility of these selections: see the
template.cpp
file in the
share/gromacs/template
directory of your installation
for an example.