Energies per Lennard-Jones interaction

Analyzing the energy contributions of each Lennard-Jones interaction pair is possible within PumMa. If this analysis is enabled, PumMa sends the energies per interaction pair to file at the same frequency as the total energy reports (hence specified by Erep in the input options file).

The name of the file that the information is reported to is set to ljoutp.pof by default, although it can be altered through the ljoutpfile option in the input file. An excerpt of the beginning of this file looks like

  IT    W-W           W-G          W-T        G-G          G-T        T-T
  0    -62105.236158 -6984.704828  15.067170 -3243.143707  63.745290 -6075.463228
  25   -62114.560338 -7081.792209  14.025786 -3218.113537  64.906704 -6019.241724
  50   -62151.704155 -7011.405641  17.816440 -3240.467936  73.733343 -6019.312019
  75   -62078.925166 -7041.669532  16.365236 -3239.301648  66.215794 -6040.923983
  100  -62115.709724 -7028.384471  20.932043 -3220.622695  65.278038 -6004.419304
  125  -62207.769050 -7051.232958  15.672371 -3266.281964  66.549996 -6065.486376
  150  -62101.289425 -7010.181901  15.521451 -3280.515069  73.969946 -6029.905421
  ...

The first line of the file gives the information on which data is stored in which column. So, in this example, the first column is the iteration number, and the remaining columns are the energy contributions to the Lennard-Jones potential arising from the pairs listed at the top of the columns (which are in this case water-water, water-head, water-tail, head-head, head-tail and tail-tail).

For our bilayer to vesicle transition research, we used this tool to show that the Lennard-Jones contribution to the potential energy of the water-water interaction decreases during the bilayer to vesicle transition, as can be seen from the figure below.

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