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

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

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