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Apr 15, 2016
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## Interactive graphical analysis with VMD
### connect to pRVS
establish a TurboVNC connection to the MPCDF remote visualization service [[as described here|MPCDF-RVS]]
### Start VMD
~>module load vmd
### Instructions for working with the GUI
predefine some default view and enable comprehensive analysis work
flows for the user
you can save and load views (screen shot 01).
you can use different graphic representations - points, bonds,
atoms as spheres, etc. (screenshots 02 and 03).
I did not find volume rendering like in Visit but the spheres may by
opaque or transparent which gives a volumetric impression.
basic user interaction:
a) start, pause, continue time evolution
you can load different molecules and switch between them (screenshots
04 and 05). I did not find any "player" functionality like in VisIt or
I just cannot use it correctly maybe.
b) rotate, transfer, zoom in or out, change the number of shown unit
all works - you can even leave the model rotating by itself - exept
"change the number of shown unit cells" - this I did not find
c) determine species type and atom number by clicking the sphere
representing that atom
you can do various types of analysis (screenshots 06, 07 and 08) but
from the menu and not by clicking on the atom. The window is not
d) change the iso-value for the density, colour scale for the
you can do changes in graphical representation like coloring method,
surface opacity, resolution, etc. (screenshots 09, 10 and 11).
select a plane and display a colour map or a contour plot of the
(interpolated) volumetric data
you can do a clipping plane (screenshot 12) but I did not find any
calculate the density integral within a 3D box selection
did not find
display distances, angles, and dihedral angles by selecting atoms
I think it is not possible
interactively replicate the unit cell
did not find.