Visualization
Together with PumMa a visualization toolkit (PumMaTK) is available. As mentioned before it can be used to set up the system to be simulated, change it (merging, cropping, multiplicating, rotating and so on) or to do some basic analysis (radial distribution functions).
However, visual analysis of a simulations trajectory can also be very important. In order to do so a conversion program has been written, which transforms the PumMa configuration files (topology, system configuration, parameters and coordinates) into files that can be read by the program VMD. The conversion program is based on Python, with some routines in C. It can be started from the commandline by typing pumma2vmd followed by the basename of the system configuration files (by default this is sys). When the program is started the following appears on the screen
Conversion of iterations 0 to 2500 (6 timesteps)...
Molecules selected:
W (6471 molecules)...
G4T4T4 (244 molecules)...
Converting PumMa configuration files... |*** |
This generates five additional files: result.dcd, result.psf, box.dcd, box.psf and script.vmd. The first file contains all frames of the trajectory and is, in general, by far the largest file of the five. The second file contains the topology (in some sort of CHARMM format) so VMD can handles the visualization. The two box-files contain similar information to the former two, although all the information is on the periodic box, so a nice orthorombic box can be drawn around the system. The final file, script.vmd contains VMD instructions on how to draw the trajectory. The easiest way to get the visualization up and running is by typing vmd -e script.vmd at the command line. This parses the VMD-script file, which subsequently reads the appropriate trajectory and topology files and sets all drawing options correct. Some snapshots of a trajectory might look like the ones below, although these have been rendered afterward with PovRay.
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