Building blocks in GROMACS are either whole molecules (e.g. water or any small organic solvent) or residues (for proteins, DNA or RNA). A fair number of these are included in the GROMACS distribution by default, but topologies for molecules or building blocks can be written fairly easy. If you happen to have written a topology for your molecule(s) or residue(s), please allow other GROMACS users (and us ofcourse) to benefit from your effort by submitting your topology to our GROMACS topology repository.

The columns describe the following:

In total there are 98 building blocks in ffgmx, of which 32 are also in ffgmx2, and another 32 could be used in ffgmx2. Additionally there are 9 building blocks in various .itp files, 5 of which have united 'carbon' atoms and should therefore preferably only be used together with ffgmx, and 4 which can be used together with either ffgmx or ffgmx2.

Note that the ffgmx2 forcefield is actually identical to ffgmx, the only difference being the mass of the protons, which is not summed into the carbons but is explicitly present on the location of the hydrogen. This requires some additional dihedral angles and some changes and additions to angles. All other parameters (Lennard-Jones, charges etc.) remain unchanged. Having all the protons is useful for calculating NOE's and NMR refinement.

If you notice errors and/or omissions in this table, please don't hesitate to mail us at gromacs@gromacs.org!