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Parameterization of novel moleculesTable of contentsMost of your parameterization questions/problems can be resolved very simply, by remembering the following two rules:
It would be wise to have a reasonable amount of simulation experience with GROMACS before attempting to parameterize new force fields, or new molecules for existing force fields. These are expert topics, and not suitable for giving to (say) undergraduate students for a research project, unless you like expensive quasi-random number generators. A very thorough knowledge of Chapter 5 of the GROMACS Manual will be required. If you haven't been warned strongly enough, please read below about parameterization for exotic species. Another bit of advice: Don't be more haphazard in obtaining parameters than you would be buying fine jewelery. Just because the guy on the street offers to sell you a "diamond" necklace for $10 doesn't mean that's where you should buy one. Similarly, it isn't necessarily the best strategy to just download parameters for your molecule of interest from the website of someone you've never heard of, especially if they don't explain how they got the parameters. Be forewarned about using PRODRG topologies without verifying their contents: the artifacts of doing so are now published, along with some tips for properly deriving parameters for the GROMOS family of force fields. Exotic SpeciesSo, you want to simulate a protein/nucleic acid system, but it binds various exotic metal ions (ruthenium?), or there is an iron-sulfur cluster essential for its functionality, or similar. But, (unfortunately?) there aren't parameters available for these in the force field you want to use. What should you do? You shoot an e-mail to the GROMACS users emailing list, and get referred to the FAQs. If you really insist on simulating these in molecular dynamics, you'll need to obtain parameters for them, either from the literature, or by doing your own parametrization. But before doing so, it's probably important to stop and think, as sometimes there is a reason there may not already be parameters for such atoms/clusters. In particular, here are a couple of basic questions you can ask yourself to see whether it's reasonable to develop/obtain standard parameters for these and use them in molecular dynamics:
If the answer to either of these questions is "Yes", you may want to consider doing your simulations with something other than classical molecular dynamics. Even if the answer to both of these is "No", you probably want to consult with someone who is an expert on the compounds you're interested in, before attempting your own parameterization. Further, you probably want to try parameterizing something more straightforward before you embark on one of these. |