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Re: Drawing BCPs and Laplacian isosurface both at the same time?

dummy@example.com (saeed_E) — Wed, 05 Mar 2025 11:42:37 +0000

Thank you very very much.

Best regards,
Saeed

Re: Drawing BCPs and Laplacian isosurface both at the same time?

dummy@example.com (sobereva) — Wed, 05 Mar 2025 10:32:05 +0000

It is correct.

Re: Drawing BCPs and Laplacian isosurface both at the same time?

dummy@example.com (saeed_E) — Wed, 05 Mar 2025 09:46:48 +0000

Dear Tian,
Please accept my highest and deepest gratitude for the highly valuable time, energy, and patience you kindly spent to guide me in the best possible manner.
Following your instruction I could draw what I was looking for.
If possible, please let me ask a conceptual question. Considering my system I used "cub Laplacian 0.0" command in the VMD main windows so that the zero value is adjusted for both positive and negative parts of the Laplacian isosurface. As you can see in the presented picture, the selected BCP is located outside the zero isovalue of Laplacian. Consequently, it means the Laplacian at this BCP should be positive. Moreover, if a given BCP is located inside the zero isosurface of Laplacian (BCP is surrounded by Laplacian isosurface whose isovalue is zero), it means that Laplacian at that point should be negative. Please, if possible, let me know if my interpretations about the sign of Laplacian are reasonable based on how a BCP is located inside or outside of isosurface.

Sincerely yours,
Saeed

Re: Drawing BCPs and Laplacian isosurface both at the same time?

dummy@example.com (sobereva) — Wed, 05 Mar 2025 07:45:25 +0000

After performing topology analysis in Multiwfn, choose "-4 Modify or export CPs (critical points)" and then "6 Export CPs as CPs.pdb file in current folder". Also, after calculating grid data of Laplacian of rho in main function 5, export it as .cub file. After that, use VMD to show .cub file as an isosurface map, and show CPs.pdb as vdW style (with very small radius scale).

Re: Drawing BCPs and Laplacian isosurface both at the same time?

dummy@example.com (saeed_E) — Tue, 04 Mar 2025 09:41:59 +0000

Dear Tian,
Too many thanks for your so valuable guidance. But please let me state that I want to do visualization using a third party. Indeed, I want to generate corresponding "cub" files and, then, using "Cub" script in the VMD to reach very nice and high quality isosurface with BCPs. Could you please guide me to know how I can reach this purpose?

Sincerely,
Saeed

Re: Drawing BCPs and Laplacian isosurface both at the same time?

dummy@example.com (sobereva) — Tue, 04 Mar 2025 09:17:38 +0000

Dear Saeed,

Use main function 2 of Multiwfn to perform AIM topology as usual, then goto main function to calculate grid data of Laplacian of rho, then when you choose option -1 in the post-processing menu to visualize isosurface, and set bond radius to 0, you will find both BCPs and isosurfaces are shown.

Best regards,

Tian

Drawing BCPs and Laplacian isosurface both at the same time?

dummy@example.com (saeed_E) — Mon, 03 Mar 2025 18:42:34 +0000

Dear Tian,
Please let me ask a question regarding an issue I saw in an interesting article.
Please suppose one wants to draw BCPs together with the Laplacian isosurface exactly as presented in the attached picture.
As you can see, the Laplacian isosurface corresponding to isovalue 0.00 (namely reactive surface) and also BCPs are portrayed together. If possible, please let me know how one can reach such a picture using Multiwfn. Indeed, while I know how to draw Laplacian isosurface (5 Output and plot specific property within a spatial region and...), I do not know how to include BCPs at the same time.

Sincerely,
Saeed