Gromacs

Analysing Trajectory Information

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    Extracting Trajectory Information

    There are several techniques available for finding information in GROMACS trajectory files.

    • use the GROMACS trajectory analysis utilities
    • use g_traj to write a .xvg file and read that in an external program as above
    • write your own C code using gromacs/share/template/template.c as a template
    • use gmxdump and redirect the shell output to a file and read that in an external program like MATLAB, or Mathematica or other spreadsheet software.

    See Plotting Data, also.

     

    Reducing Trajectory Storage Volume

    First, consider whether you are producing more output than you need to store. Look at the .mdp file options for output frequency of positions (nstxout) and velocities (nstvout) in .trr files, whether you should be using .xtc files (nstxtcout), and whether you should be outputting only subsets of your system (output control) .

    With GROMACS 3.x you normally only want a full frame of positions and velocities in your .trr file with frequency with which you might ever want to do an exact restart (and make sure your energy output frequency (nstenergy) is a suitable multiple so you also have energies at this time). This frequency is invariably much smaller than the frequency with which you want output data. If you only want position data for your solute for your later analysis, then outputting only that group to an .xtc file (xtc_grps) with frequency (nstxtcout) as high as you'd ever need will be a tiny fraction of the cost of a .trr file of the whole system with positions and velocities at every step. You can still have your .trr file for restarts - they're independent. Be aware that analysis types that require autocorrelation functions need data sampled much more frequently than the characteristic times of the system.

    With GROMACS 4.x the above is superseded by the checkpointing mechanism.

    Note that you can also use trjconv and eneconv to reduce your output frequency, change file format and select groups after doing the simulation too, but most of these decisions are best made (correctly!) before the simulation.

     

    Resources

    • Analysis of MD trajectories in GROMACS (slides,video) - (David van der Spoel).
    Page last modified 18:25, 9 Oct 2009 by JLemkul?