How to create lipid-protein complex rendering in VMD

This tutorial talks about how to make this figure in VMD:

Visualize Lipids and Ligand in the Protein Complex

My device has an AMD 3950x CPU with 2 NVIDIA 2070S GPUs. I use Ubuntu 20.04 and VMD version 1.9.4a38. Besides this information to give you clues if something does work as I show here, all the following steps shall work on any system setup.

First, make a few systematic settings:

• ‘Display->Rendermode’, choose GLSL, which produce more beautiful figures than default Normal;
• ‘Graphics->Colors->Display->Background’, choose ‘8 white’;
• ‘Graphics->Colors->Type->C’, choose ‘6 silver’, this is for giving a dark, solemn feeling of the lipids;

Second, select lipids, ligand, and protein separately.

• Protein: color by ‘ColorID->8 white’, ‘NewCartoon’, material ‘Transparent’;
• Lipids: color by ‘Type’, ‘vdw’, material ‘AOChalky’;
• Ligand: color by ‘Name’, ‘vdw’, material ‘AOShinny’;

Third, modify the material properties for ‘Transparent’, ‘AOChalky’, ‘AOShinny’.

Adjust Outline, OutlineWidth, Opacity for ‘Transparent’ type

Adjust Outline and OutlineWidth for ‘AOChalky’ type

Adjust Outline and OutlineWidth for ‘AOShiny’ type

Third, adjust the ‘Display->Display Settings’.

We decrease ‘Near Clip’ to 0.01, the smallest value, and turn on ‘Amb Occl’ and ‘Shadows’. The values of ‘AO Ambient’ and ‘AO direct’ should add up to more than 1 to yield bright enough view.

Adjust Display Settings

Fourth, I use Tachyon-Optix (internal, GPU-accelerated) to render the figure. It was pretty fast, about a few seconds for each frame. Using Tachyon (internal) is very slow, as it uses all the available CPU for rendering (as shown below), and takes several minutes to finish one.

All the CPU Cores are Occupied for Rendering Job

Then you will get this figure:

Congrats!