Gromacs

Multiple Topology Entries

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    In some situations it may be required to produce a more complex bond term than the standard form provided. This can be achieved by combining multiple terms, which then add up to the final bonding term required.  This technique can be of use, for example, when a dihedral potential function follows the Ryckaert-Bellemans function but has additional terms present beyond the standard n=5 in GROMACS.

    The topology file entries within the [ bonds ], [ pairs ], [ angles ] and [ dihedrals ] sections are all additive, with each additional entry added to the previous one.  Duplicating a term here will double the resulting potential energy term (without warning!), so modify carefully.

    Do not confuse this mechanism with defining bonded types (i.e., [ bondtypes ], [ angletypes ], and [ dihedraltypes ]) in your ffbonded.itp file; multiple terms in these directives will over-write any previous instance, leading grompp to fail with a warning.  The exception to the rule is the CHARMM force field.

    Page last modified 13:42, 7 Dec 2010 by JLemkul?