How do I use Martini 3 with GROMACS? #7
CeraveWasTakenLOL
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While Martini has been (principally) optimised to be run with gromacs, this doesn't mean that Martini is native to gromacs. For example pdb2gmx won't be able to just make a protein structure, because the atom names in rtp files don't correspond to martini bead names. For this purpose, the martini community develops tools like martinize2 to generate coarse-grained topology files as inputs that gromacs can read (in short, generate tpr files to run simulations with). The collection of tutorials that we've developed might be a good place to start to see how this can work in practice if you're already familiar with gromacs. |
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I downloaded Martini 3 and moved it to my force field directory but GROMACS doesn't recognize it. This has not been an issue with any other force field I've downloaded.
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