how to visualize bader result with VMD

Bader charge density analysis

Moderator: moderators

how to visualize bader result with VMD

Postby jiddy » Thu May 19, 2011 8:44 pm

Hi I ran Bader on the gaussian cube file which contains charge density using the following command.
bader [cube file]
THe following three files were generated: BCF.dat; AVF.dat; ACF.dat. Is AVF.dat the volume file? How do I visualize it in VMD?
jiddy
 
Posts: 4
Joined: Thu May 19, 2011 8:35 pm

Re: how to visualize bader result with VMD

Postby graeme » Tue May 24, 2011 1:22 am

You can print the Bader volumes using the -p option and view the chgcar/cube style files. Each volume can be printed with a non-zero value in the volume and zero outside. Setting a low value for an isosurface in vmd will show you an outline of the Bader volume.
graeme
Site Admin
 
Posts: 1056
Joined: Tue Apr 26, 2005 4:25 am
Location: University of Texas at Austin


Return to Bader

Who is online

Users browsing this forum: No registered users and 1 guest

cron