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make ndxTable of contents
Almost every GROMACS program can utilise an index group for its operation and make_ndx can generate the index file. Such groups are only required when specialty subsets of atoms are required, since default index groups are already generated (entire system, 9 groups for proteins, and one for every other residue name). The program allows you to select by atom, residue and chain names and numbers (or atom type when supplying run input file). You can use NOT, AND and OR, split groups into chains, residues or atoms, and delete and rename groups. Example UsageTyping "h" at the make_ndx prompt will give some good examples of how to use the tool. A common request across the gmx-users listserv is to provide examples of how to create special index groups. There are some examples in the list archive, but a concise presentation of a few is appropriate here. Since membranes tend to give the most issues, these examples are in the context of a fully-solvated, pure DPPC bilayer. For tools like g_density, dividing the lipids into different regions is common. To create a group containing just headgroup atoms: > a C1 | a C2 | a C3 | a N4 | a C5 | a C6 | a O7 | a P8 | a O9 | a O10 | a O11 This will be entered as Group 3, so, for convenience, you could enter the following: > name 3 Headgroups To analyze, for example, the properties of the headgroups of one leaflet, first create a group that contains just the lipids of the top leaflet (assuming a 128-lipid bilayer, this would correspond to residues 1-64). > r 1-64 Found 3200 atoms with res.nr. in range 1-64 3 r_1-64 : 3200 atoms > 3 & a C1 | a C2 | a C3 | a N4 | a C5 | a C6 | a O7 | a P8 | a O9 | a O10 | a O11 (some listing of how the groups are being merged) 4 r_1-64_&_C1_C2_C3_N4_C5_C6_O7_P8_O9_O10_O11: 704 atoms > name 4 1-64_Headgroups Another common question is about how to create the proper index group for deuterium order analysis. Please see the g_order page for information on how to properly create these groups.
Reference
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