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

    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, so neither of those procedures are recommended.

    Page last modified 00:35, 12 Jul 2012 by mabraham