Automatic selection of ELF basins

mverissi · 2024-11-02 02:26:49

Dear Prof. Lu,

I intend to use Multiwfn to plot ELF functions to try to understand how catalysis takes place in the active site of a DNA polymerase. I have performed QM/MM calculations with ORCA and I have successfully plotted ELF isosurfaces in VMD.

I will plot the ELF functions for each image in an NEB calculation with many images (about 60!) and hopefully attempt to detect changes in the basins along the reaction coordinate determined by the NEB calculation.

Looking in the manual, I saw how one can plot monosynaptic and disynaptic basins in different colors. It might be a good idea to do this, since perhaps I could detect changes in these basins visually.

I have 197 atoms in my quantum region, and I performed a calculation with the coarsest grid, just to see the sequence of options that I would input in a submission script to automate the execution. However, I was a bit disappointed when I realized I'd have to input the numbers of the basins, and that there's no option to select all basins for output.

With the current workflow, I suppose that, to automate the calculation, I would have to perform the basin calculation redirecting the MWFN output to a file. Then I'd have to interrupt it to get the indices of the N-synaptic basins from the MWFN run, and input them in a second run. That would, of course, be a waste of computer time. Is there any other way to tell MWFN to save a cube file with all the basins?

If there's no way to do this, although my Fortran is a bit rusty, I suppose I could try to look into the code and attempt to adapt it if necessary. Could you kindly point me to which files I should look into?

Best regards,

Marcos Verissimo Alves

sobereva · 2024-11-02 15:23:12

Dear Marcos Verissimo Alves,

Some suggestions:

1 In option "-5 Export basins as cube file", you can use command "a" to export basin.cub, which contains information of all basins.

2 Your quantum region is large, but the reactive region should be much smaller than this size. In the step of "Please select a method for setting up grid", you can consider to choose "8 Set center position, grid spacing and box length", and properly set the center and length of the box so that only reactive region is covered by the grids, the computational cost should be significantly lower than computing the entire quantum region.

3 To avoid calculating grid data twice, you can first use main function 5 to generate grid data for the reactive region, and export the grid data as a cube file, and then return to main menu, enter main function 17 and select 1 to generate basins, then choose "2: Generate the basins by using the grid data stored in memory". This run you can obtain indices of the basins of interest as usual. In the next time of running Multiwfn, you can use the cube file as input file, then still choose "2: Generate the basins by using the grid data stored in memory" when performing basin anaylsis.

Best regards,

Tian

mverissi · 2024-11-02 19:16:24

Dear Prof. Lu,

Thank you for the tips. I will try them out and share what happened so that other users may benefit from this knowledge.

Best,

Marcos

mverissi · 2024-11-29 02:35:23

Dear Prof Lu,

I finally had the time to try what you suggested (loading the grid from the cube file and using the grid data stored in memory to re-generate the basins), except for the part of selecting a smaller part of my quantum region. The reason is that I will still have a large region to look at (I am analyzing the breaking of a P-O bond of a deoxyribonucleotide triphosphate).

When I select option 2 ("Generate the basins by using the grid data stored in memory"), MWFN outputs all the points on the screen. Even if I select a smaller region, I will still have a massive number of points when I select a finer grid, and outputting them on screen will certainly slow the calculation down. Is there any way of suppressing this output?

Best,

Marcos

sobereva · 2024-11-29 15:01:12

Dear Marcos,

Simply printing the located attractors on screen doesn't notably slow down the calculation, the most time-consuming part is generating the attractors/basins.

Perhaps, what you need is an option, by which you can directly load the information of previously located attractors and attribution of grids to basins, so that you can avoid regenerating the attractors/basins in the second run? If yes, I can add it.

Best,

Tian

mverissi · 2024-11-30 14:54:56

Dear Prof. Lu,

That would be immensely valuable. It would potentially save up to a day or so in computing time. I would have to run this for many geometries to keep track of the changes in valence basins from one image of the NEB calculation to the next. Thanks for your kind offer — I'll be eagerly awaiting the release of this feature.

Best,

Marcos

sobereva · 2024-12-01 18:10:38

Dear Marcos,

I just updated Multiwfn today. A new option -45 has been added to basin analysis module. Description of this option in the updated manual:

-45 Export attractor information and cube file of present grid data: This option is available when attractors and basins have been generated. By this option you can export attractor and basin information as basinana.txt in current folder and export present grid data as basinana.cub in current folder. When you perform the same basin analysis next time, after choosing option 1 to try to generate basins, if the two files are found in current folder, Multiwfn will ask you if directly loading them; if you choose y, the attractor&basin information as well as grid data will be loaded, and hence the cost for regeneration of them is fully avoided.

Best regards,

Tian

mverissi · 2024-12-06 16:25:51

Dear Prof. Lu,

I apologize for not replying before — I didn't expect the update so soon! Is this option in the compiled version of Mwfn?

Best,

Marcos

sobereva · 2024-12-06 17:25:26

Dear Marcos,

Yes, it is already available in the precompiled binary version of Multiwfn.

Best,

Tian

mverissi · 2024-12-06 18:53:08

Wow, that's awesome! I can't thank you enough, and I'll try it ASAP!

Best,

Marcos

Multiwfn forum

#1 2024-11-02 02:26:49

Automatic selection of ELF basins

#2 2024-11-02 15:23:12

Re: Automatic selection of ELF basins

#3 2024-11-02 19:16:24

Re: Automatic selection of ELF basins

#4 2024-11-29 02:35:23

Re: Automatic selection of ELF basins

#5 2024-11-29 15:01:12

Re: Automatic selection of ELF basins

#6 2024-11-30 14:54:56

Re: Automatic selection of ELF basins

#7 2024-12-01 18:10:38

Re: Automatic selection of ELF basins

#8 2024-12-06 16:25:51

Re: Automatic selection of ELF basins

#9 2024-12-06 17:25:26

Re: Automatic selection of ELF basins

#10 2024-12-06 18:53:08

Re: Automatic selection of ELF basins

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