Gromacs

Single-Point Energy

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    Computing the energy of a single configuration is an operation that is sometimes useful. The best way to do this with GROMACS is with the mdrun -rerun mechanism, which applies the model physics in the .tpr to the configuration in the trajectory or coordinate file supplied to mdrun.

    mdrun -s input.tpr -rerun configuration.pdb
    

    Note that the configuration supplied must match the topology you used when generating the .tpr file with grompp. The configuration you supplied to grompp is irrelevant, except perhaps for atom names. You can also use this feature with energy groups (see manual), or with a trajectory of multiple configurations (and in this case, by default mdrun will do neighbour searching for each configuration, because it can make no assumptions about the inputs being similar).

    A zero-step energy mInimization does a step before reporting the energy, and a zero-step MD run has (avoidable) complications related to catering to possible restarts in the presence of constraints, so neither of those procedures are recommended.

    Page last modified 13:35, 25 Jun 2015 by mabraham