VMD Cheat Sheet - Harvard University

VMD Cheat Sheet



For version 1.9.3. by Lixin Sun at MIT. contact: nw13mifaso@

GUI-interface

Load a molecule

Control panel Files New molecules

Add a layer of selected atom ( i.e. "sqrt((x-2)**2+(y2)**2)4 and type 2")

Delete a layer

Change background color

Change view

Control panel Graphics Representation create Rep type "sqrt((x-2)**2+(y2)**2)4 and type 2" in "Selected Atoms"

Control panel Graphics Representation select the layer Delete Rep. (or double

click to just hide the layer) Control panel Graphics color

Display Background Control panel Display perspective /

orthographic

TK Console

mol new type

mol selection {sqrt((x-2)**2+(y2)**2)4 and type 2 }

mol addrep top

mol delrep 0 top

color Display {Background} white display projection Orthographic

or display projection Perspective

note

In terminal: $vmd a.lammpstrj For VASP output POSCAR / CONTCAR, the automate detection won't work. You need to select file type manually

Change coloring method

Control panel Graphics Representation select "Coloring method" as "ColorID"

mol color ColorID 0 then redefine the current presentation

Change drawing method

GUI-interface

TK Console

note

Control panel Graphics Representation select "Drawing method" as "cpk" or "point" or line

mol representation CPK

Change transparency of atoms

Read coordination

Read bond length

Rotate configuration

Output / render image Change default setting Save the current setting in a file Load a previous setting

Control panel Graphics Representation select "Material" as "Transparent"

Visualization window keyboard "1" mouse click

Visualization window keyboard "2" mouse click

Keyboard "R" use mouse Keyboard g/h/j/k/l

Control panel Files Render choose the software, usually povray or tachyon

Control panel Extension VMD preference

Control panel File save visualization state

Control Panel File load visualization state

mol material

rotate y by 90 render Tachyon outputfilename " ................
................

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