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