Gromacs knows about several standard groups that you can often select when you work with the Gromacs analysis tools.
The standard groups are:
|System||all atoms in the system|
|Protein||all protein atoms|
|Backbone||protein backbone atoms: N, Cα and C|
|MainChain||protein backbone atoms: N, Cα, C and O, including oxygens in C-terminus|
|MainChain+Cb||protein main chain atoms including Cβ|
|MainChain+H||protein main chain atoms including backbone amide hydrogens and hydrogens of the N-terminus|
|SideChain||protein side chain, that is all protein atoms except N, Cα, C and O, backbone amide H and H at the N-terminus, O at the C-terminus|
|Prot-Masses||needed in connection with virtual sites when one wants to excludes dummy masses (which are included in the "Protein" group)|
|Non-Protein||all non-protein atoms|
|DNA||all DNA atoms|
|RNA||all RNA atoms|
|Water||water molecues (names like SOL, WAT, HOH, etc.), see "residuestypes.dat" for full listing|
|non-Water||anything not covered by the "Water" group|
|Ion||any name maching an "Ion" entry in "residuestypes.dat"|
|Water_and_Ions||combination of the "Water" and "Ions" groups|
|molecule||for all residues/molecules which are not recognized as proteinm DNA or RNA, one group per residue/molecule is generated (for example: four HEME groups are generated if one simulates hemoglobin)|
|Other||all atoms which are neither protein, DNA, nor RNA|
Groups that do not belong to the default groups can be generated using
make_ndx. For instance, if we are interested in how the distance between the Cα atoms of the N- and C-terminal residues evolves with time, Gromacs needs to now the indices of these atoms in the trajectory. You can create the corresponding group with
gmx make_ndx -f md_protein.tpr -o NC_distance.ndx
3 & ri 1 18
3 & r 1
3 & r 18
enter again to list the defined groups.
The new group will appear at the end.
You can write everything to the previously specified file
NC_distance.ndx by entering
ri refers to the "residue index" and the tool will take the corresponding residue in order,
r corresponds to the residue numbering in the input file. With
one can delete groups, e.g.,
del 0-9 deletes the default groups 1-9, only leaving the newly defined
groups in the example above. The resulting file
NC_distance.ndx is a text file containing the groups.
The name of each group is written between square brackets, followed by the atom numbers (which can be spread out over several lines)
belonging to the group in question. All following
gmx analysis commands can be invoked together with the
-n flag and a user supplied index file, such as
this flag, only the standard groups given above are available.