Gromacs

GROMOS

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    GROMOS is is a general-purpose molecular dynamics computer simulation package for the study of biomolecular systems. It also incorporates its own force field covering proteins, nucleotides, sugars etc. and can be applied to chemical and physical systems ranging from glasses and liquid crystals, to polymers and crystals and solutions of biomolecules.

    GROMACS supports the GROMOS force fields, with all parameters provided in the distribution for 43a1, 43a2, 43b1, 45a3, 53a5 and 53a6. The GROMOS force fields are united atom force fields, i.e. without explicit aliphatic (non-polar) hydrogens.

    It is also worth noting the inclusion of the so-called "ffgmx" force field, which is somewhat of a derivative of the GROMOS87 force field.  Warnings to its "deprecated" status are given in the manual and by pdb2gmx.  Users are advised not to use this particular force field - it is outdated and poorly documented.  Specifically, see here.  There is no such thing as a "GROMACS force field," although it has (unfortunately) become commonplace to refer to ffgmx as such.

    Page last modified 01:53, 9 Mar 2010 by mabraham