Re: Extract coordinates from fragments in batches

dummy@example.com (sobereva) — Thu, 05 May 2022 02:57:08 +0000

You may use geometry operation function in Multiwfn to realize this. For example, you want to extract atoms 2,5-9 from old.xyz to new.xyz, you can boot up Multiwfn and input

old.xyz
300
7 // Geometry operation
17 // Crop some atoms
2,5-9
-1 // Save current geometry to a .xyz file
new.xyz

Now you have new.xyz in current folder. You can use your script to automatically run above commands for a batch of systems.

Extract coordinates from fragments in batches

dummy@example.com (Hans) — Wed, 04 May 2022 23:44:20 +0000

Best regards. I want to make use of the sub function 0 (custom operation) of the main function 5 (calc. grid data) of Multiwfn for each point of a reaction coordinate, my problem is to extract the coordinates of the fragments from a file containing the coordinates of the molecular system for each point of the IRC (for example from a xyz format file), see attached image.
I tried to do this using BATCH commands, but I am not very good at this. I don't know if you could provide me with a suitable BATCH program for this purpose.
PS: I am a Windows user only.
Thanks in advance.