Talk:Mod:Hunt Research Group/VMDReminder

Quick reminder

• this section is only if you need a reminder, the following sections are if you are a complete beginner

Reading in a File

• you will need a molecule or trajectory file

the most common formats are xyz coordinates or a history file from dlpoly

copy the file to your local computer

• start VMD
• to load a file

select "File" then "New Molecule"

"Browse" and choose a file, this can be *.xyz a dlpoly HISTORY file or many other formats

if using a HISTORY file select DLPOLY V2 as the file format

now "Load" the file

Changing defaults on model rendering and colour options

• change the graphical representation to CPK

graphics:representations:CPK

• change the colours of the atoms

graphics:colours:categories:name:C:grey

• change the background

graphics:colours:categories:display(first item on list):background:black

A Quick way to identify commands

• Turn on the TkConsole and log commands

go to Extensions and turn on the TkConsole

then goto File and select log Tcl commands to Console,

or type "logfile console" in the Tcl window

this logs the command of anything you do on the GUI and thus allows you to quickly determine commands

Useful commands

• to hide a molecule double click on the "D" under molecule in the main VMD window
• to reset the display type display resetview in the console
• to scale the current image scale by x
• if you want selections to update every frame 'trajectory' and then Update selection/Update colour every frame
• rotate about a specific atom under 'mouse' =>'center' then click directly on the atom you want
• you want to "slice" through a cell, in the selection box put for example x < 0.5

Finding and labelling distances

• on the 'mouse' tab select 'query', then click on an atom and then look in the VMD terminal window
• on the 'mouse' tab select 'label'=>'bond' then click on two atoms, if you rotate the molecule you might need to click on label again
• if you want to move or hide the labels that VMD adds, under the 'graphics' tab select 'labels'=>bonds

then hide show the various bounds to work out which is which

click the properties tab and move the small circle to move the label around

• to get a graph of a particular bond/angle clikc on the 'graph' tab and then click the 'graph' button

you can save this graph or the data

Saving an Image

• file:render choose snapshot (.tga) select directory and click start rendering.
• use photoshop to convert files to other formats.

Finding the RDF

• the VMD manual http://www.ks.uiuc.edu/Research/vmd/plugins/gofrgui/
• under 'extensions'=>'analaysis'=>'radial pair distribution functions'

a window will open

in 'use molecule' choose the trajectory to analyse

in the selections put the selection method and name of the atoms ie name CR or another selection option

if you are using a *.xyz file you will need to enter the cell dimensions manually, click on the "utilities" button and input the data

click on 'compute'