Gromacs

Parameterization of novel molecules

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    Version as of 22:35, 23 Sep 2020

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    Most of your parameterization questions/problems can be resolved very simply, by remembering the following two rules:

    1. You should not mix and match force fields. Force fields are (at best) designed to be self-consistent, and will not typically work well with other force fields. If you simulate part of your system with one force field and another part with a different force field which is not parameterized with the first force field in mind, your results will probably be questionable, and hopefully reviewers will be concerned. Pick a force field. Use that force field.
    2. If you need to develop new parameters, derive them in a manner consistent with how the rest of the force field was originally derived, which means that you will need to review the original literature. There isn't a single right way to derive force field parameters; what you need is to derive parameters that are consistent with the rest of the force field. How you go about doing this depends on which force field you want to use. For example, with AMBER force fields, deriving parameters for a non-standard amino acid would probably involve doing a number of different quantum calculations, while deriving GROMOS or OPLS parameters might involve more (a) fitting various fluid and liquid-state properties, and (b) adjusting parameters based on experience/chemical intuition/analogy.

    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 strongly enough warned, please read this page about parameterization for exotic species.

    A final bit of advice: Don't be more any 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.

    Page last modified 08:27, 19 Mar 2009 by rossen