RMSF to B-factor conversion

GROMACS version: 2020.4
GROMACS modification: No

Hi everyone,

I was wondering if anyone knew the exact calculation that is used in the ‘gmx rmsf’ when using the ‘-oq’ option to have the RMSF values converted to B-factor values, which are written to a .pdb file?

I have messed around doing the calculation manually with this equation that I had found:


However, my final values end up being off by a factor of 100, which I’m guessing is simply an error in units or something of that sort.

Any help would be greatly appreciated!


Probably nm2 → Å2.

That would do it!

So I’m guessing ‘gmx rmsf’ automatically converts from nm^2 to angstrom^2 with the ‘-oq’ option.

Thank you!

Yes, because GROMACS operates in SI units but for PDB compliance the values are written in Å2.