Large .gro files

User discussions
1

Hello everyone,

There’s a limit to gro file dimensions?
How can I renumber residues or atoms when they’re more than 100k as there’s the 5 integer limit for gro file format?

Thank you in advance and have a nice day
Matteo

2

Hi,

as far as I know there is no limit on box dimensions or number of atoms. The indexing does not seem to matter for Gromacs itself, so you can renumber the indices by doing modulo 100000: i = i % 100000. That keeps the index within the five-digit format.

Regards,
Petter

3

Thank you for the input,

Does that mean that after 99999 I just recount as 0,1,etc?

Cheers
Matteo

4

Indeed, just so. That’s precisely what I’ve done to simulate systems with millions of atoms. And it’s how the .gro files which Gromacs writes with more atoms than 100k are formatted.

Petter

5

Okay, thank you again!