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g energy

    Table of contents
    1. 1. Using g_energy
    2. 2. Reference

    The g_energy program extracts information from .edr files and prints the output to an .xvg file for plotting and / or further analysis.

    You will notice that three kinds of Lennard-Jones energies may be reported. When calculating the non-bonded energies, GROMACS can handle twin-range cutoffs, depending on the settings in the .mdp file (and see the manual), so LJ-SR ("short-range") is the LJ contribution inside the shortest cutoff, and LJ-LR ("long-range") is outside the shortest cutoff, but within the longest. LJ-14 is the pair interaction contribution.

    Analogously, energy terms for Coulombic interactions are also present in various forms.  Coul-SR is the Coulombic potential within rcoulomb.  Coul-14 is the pair interaction contribution.  The Coul-LR term is written when (rlist = rvdw) < rcoulomb.  Long-range electrostatics are calculated by various methods (PME, Reaction Field, etc) and thus show up as different terms, such as Coul-recip in the case of PME, a term that cannot be decomposed, regardless of the energygrps specified in the .mdp file.

     

    Using g_energy

    To get g_energy to print useful interaction, the user must specify the energy terms to be written to the output file.  The program will print a list of all energy terms contained in the .edr file, from which the user can choose.  The user then must enter either the number(s) corresponding to the desired energy term(s) or the desired name(s), followed by 0 (zero) or a blank line to terminate selection, and finally 'Enter.'  Selections can also be made non-interactively.

     

    Reference

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    Page last modified 23:33, 2 Oct 2012 by JLemkul?