Gromacs

Force Fields

    Table of contents
          1. 1.1.1.1. Table of contents
    1. 2. Types
    2. 3.
    3. 4. Usage
    4. 5.
    5. 6. Force Fields in GROMACS
    6. 7.

    A force field is built up from two distinct components to describe the interaction between particles (typically atoms):

    • the set of equations (called the potential functions) used to generate the potential energies and their derivatives, the forces.
    • the parameters used in this set of equations

     

    Types

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    There are three types of force fields:

    • all atom - parameters provided for every single atom within the system.
    • united atom - parameters provided for all atoms except non-polar hydrogens.
    • coarse grained - an abstract representation of molecules by grouping several atoms into "super-atoms".

    Usage

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    Within one set of equations, various sets of parameters can be used. Care must be taken that the combination of equations and parameters form a consistent set (see: Parameterization). It is generally dangerous to make ad hoc changes in a subset of parameters, because the various contributions to the total force are usually interdependent. In particular, there is no reason to suppose that treating part of your system with one force field and part with another force field will lead to results that have any meaning at all. There is also no reason to suppose that a force field's "bond strength" parameter has any particular correlation with any real measure of the strength of such a bond.

    As a good starting point for more details, read the GROMACS manual, which has a detailed chapter on force fields - what they are, how they are implemented, etc.

    For parameterization of novel molecules, first consult the following information.

    Page last modified 21:07, 28 Dec 2010 by mabraham