zako 发表于 2019-12-5 20:57
First, thank you very much for the tutorial, i learn a lot of things.
Please Prof. Sobereva, see th ...

You should use Tachyon render to realize anti-aliasing effect. Select: File - Render - Tachyon (internal, in-memory rendering)
Alternatively, you should enable anti-aliasing effect in the setting panel of your graphical card.

zako 发表于 2019-12-5 00:06
Thank Prof. Sobereva,
A wonderful tutorial. Please I have another question concerning the backgroun ...

Select "Display" - "Depth Cueing" to disable the depth cueing effect

Thank Prof. Sobereva,
A wonderful tutorial. Please I have another question concerning the background of vmd.
In vmd i work with a black background  until i finish all the tasks, but when i change the color of background to withe color the atoms became less clear than they was in the black background. How can i fix this thing.

I strongly suggest you watch this video tutorial, which contains the step of using the .vmd script.

Using Multiwfn to perform NCI analysis to reveal intra- and intermolecular interaction
https://youtu.be/e4FpVc9ao48

zako 发表于 2019-12-3 20:52
Dear snljty, Please see the screenshot

That is because it is a script file, not a molecule description file. You need to source this script using command "source PhenolDimer.vmd" in the console window.

There are two "set" statements in your script line 4 and 5, but there are no values provided.
Generally the syntax should be "set varName newValue".
I cannot see following reference of these two variables, just try to delete or comment these two lines.
You'd better upload the error message and your files PhenolDimer-dens.cube and PhenolDimer-grad.cube.