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Re: Using VMD for visualization of Isosurface (NCI Tutorial)

dummy@example.com (hadimohammadi13) — Sun, 22 May 2022 00:01:16 +0000

Thank you so much your comment was helpfully.

Re: Using VMD for visualization of Isosurface (NCI Tutorial)

dummy@example.com (sobereva) — Sat, 21 May 2022 18:28:04 +0000

hadimohammadi13 wrote:

Hi guys
I am going to perform NCI and AIM analysis as same as Akhila. Unfortuntly, when used cmd of VMD I have faced to such a problem. So that is there any one help to me? Additionally, you can see my screenshot here.
Thanks in advance
https://i.postimg.cc/LgDRyjb3/VMD.jpg

Please use VMD 1.9.3

VMD 1.9.4 has not been formally released yet, its current development version is quite buggy, never use it.

Re: Using VMD for visualization of Isosurface (NCI Tutorial)

dummy@example.com (hadimohammadi13) — Sat, 21 May 2022 17:52:52 +0000

Hi guys
I am going to perform NCI and AIM analysis as same as Akhila. Unfortuntly, when used cmd of VMD I have faced to such a problem. So that is there any one help to me? Additionally, you can see my screenshot here.
Thanks in advance

Re: Using VMD for visualization of Isosurface (NCI Tutorial)

dummy@example.com (sobereva) — Fri, 17 Sep 2021 17:42:19 +0000

akhila wrote:

I am trying to both NCI analysis to reveal intra- and intermolecular interaction (NCI and AIM). I have done AIM analysis. The video is very useful but I'm not getting every step of NCI and AIM. I am working on a Linux machine. Please guide me to do both NCI and AIM

I don't know what problem you have encountered. Please make sure that you are able to normally respectively plot a NCI map and a AIM map. If there is any specific problem that you cannot overcome, please explicitly let me know. To plot NCI map under Linux, you can use exactly the same script (examples\RDGfill.vmd) as my video.

Re: Using VMD for visualization of Isosurface (NCI Tutorial)

dummy@example.com (akhila) — Fri, 17 Sep 2021 12:36:48 +0000

I am trying to both NCI analysis to reveal intra- and intermolecular interaction (NCI and AIM). I have done AIM analysis. The video is very useful but I'm not getting every step of NCI and AIM. I am working on a Linux machine. Please guide me to do both NCI and AIM

Re: Using VMD for visualization of Isosurface (NCI Tutorial)

dummy@example.com (sobereva) — Thu, 22 Jul 2021 10:50:19 +0000

First, please do not use such a very old version of VMD, please use the latest formal version of VMD, namely 1.9.3

You should move RDGfill.vmd script to VMD installation folder, the folder in your screenshot is evidently not the VMD installation folder. In the VMD installation folder you should be able to find vmd.exe.

Please carefully this video tutorial:
Using Multiwfn to perform NCI analysis to reveal intra- and intermolecular interaction
https://youtu.be/e4FpVc9ao48

Using VMD for visualization of Isosurface (NCI Tutorial)

dummy@example.com (gregoryput) — Thu, 22 Jul 2021 08:49:38 +0000

Hi,

I am trying to visualize the isosurface of the example molecule Phenol Dimer in VMD after importing appropriate wfn file, executing the exact commands in Multifwn.exe as shown in tutorial and importing the RDGfill.vmd, func1.cub and func2.cub files into created VMD folder. VMD doesn't display the molecule when I execute the source rdgfill.vmd command. I think it might be because the contents of my VMD folder don't have many of the files shown in the tutorial. I need help.