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Showing posts from March, 2016

VMD High Resolution Image and Movie

Image
A nice wiki can be found here . The followings are my take home notes from various blogs and wikies. High resolution image Here are some steps which I usually follow to make high quality image from VMD. Set the visualization screen (vmdscene) according to requirement Render the vmdscene  using tachyon mode. File -> Render -> Tachyon Change the default Render command to have something like "/tachyon_path/tachyon_exe" -aasamples 12 %s -format TGA -res 1024 1024 -o %s.tga (The resolution can be tuned by changing the value for -res option (which is 1024 1024 in this case). Enable Ambient occlusion lighting in the Display -> Display Settings window by selecting "on" in "Amb. Occl" and "Shadows" choosers. If AO effect is being used, the choice of  material also affect the final visual effects. Use  "Diffuse", "AOshiny", "AOChalky", or "AOEdgy" materials. If th

Handling multi column data in xmgrace

Let say the data file contains 5 columns and we would like to plot the following 1. Column 1 vs column 3, the correct syntax is   xmgrace -block file -bxy 1:3 2. Column 1 vs. all other columns    xmgrace -nxy file