A number of molecule topologies are included in the GROMACS distribution, see our overview of Building Blocks. However, when you have worked with GROMACS for a while and applied it to your own area of research you might have had to write topologies for the molecule(s) you are working with. This could be anything from a solvent, a special aminoacid residue (e.g. with modified sidechain, or a beta-aminoacid) to a enzyme substrate or inhibitor. Hard-core simulators might even use their own force fields.

Chances are that somebody else is, or will be, working with the same systems. Since we belive it's just plain stupid to hack a new topology when it already exists, we have set up this repository of GROMACS molecule and force field and topologies contributed by users. You can find these on the Download/Upload page on categories Molecule Topologies and Force Field Topologies.

Please, try to use them! If you hesitate in giving away things that you invested (maybe quite some) work in, consider the amount of work you could have saved if someone else happened to have done it already and made it available to you.

You don't have to provide your name and e-mail adress, but we would prefer to give other people the opportunity to ask questions to you concerning your files. If all goes well, we will eventually have a (long) list of molecules appearing on this page, ready for downloading for those who need them.

If you have a ligand for your protein, or another small molecule for which no ready topology can be found, please try the PRODRG topology generation server. It generates topologies for the GROMACS force field from coordinates or a schematic drawing. These topologies are usually a good starting point to write your own. For more information, check chapter 5 of the GROMACS manual