GitLab

Interactive graphical analysis with VMD

connect to pRVS

as described here

Start VMD

~>module load vmd
~>vglrun vmd

Instructions for working with the GUI (assessment of UseCase1 is work in progress)

1. predefine some default view and enable comprehensive analysis work flows for the user (Fig 1).

• save and load views.
• use different graphic representations - points, bonds, `VDW'
• atoms as spheres

2. basic user interaction: a) start, pause, continue time evolution

• load different molecules and switch between them (screenshots 04 and 05).
• no default "player" functionality like in VisIt or ParaView

b) rotate, transfer, zoom in or out, change the number of shown unit cells

• all works

c) determine species type and atom number by clicking the sphere representing that atom

• types of analysis (Figs 2,3,4) but from the menu and not by simply clicking on the atom. The window is not interactive.

d) change the iso-value for the density, colour scale for the volumetric data

• not yet identified

4. calculate the density integral within a 3D box selection

• not yet identified

5. display distances, angles, and dihedral angles by selecting atoms

• not yet identified

6. interactively replicate the unit cell

• not yet identified