Units with colvars module

User discussions
1

GROMACS version: 2021.6-Colvars-2022-12-16-dev
GROMACS modification: No
Hi all,
a probably silly question to be sure I understood correctly the ref manual: when defining distance in colvar file, if I do not specify the keyword “units”, it is assumed that the unit is nm, so if I have to define an upper boundary of 60 angstrom, I should use 6, is that correct?

Thanks in advance

2

Correct, when using GROMACS the only allowed value would be units gromacs, which is the default anyway so you don’t need to specify it.

Other values should give you an error: if they don’t, please report it as a bug.

Giacomo

3

Hi Giacomo,
thanks for further clarification.

Stefano

4

Hey there,

I was hoping to follow up on this. Just because I am getting SUPER confused by the fact that the units of colvars are in nanometers, but in the manual here, they discuss the units of the grid and harmonic wall in angstroms.

Is this a typo or is there some conversion?

Thanks,
Shanil :)

5

Hi Shanil, apologies for the confusion. We made all the keywords and their documentation consistent with the units of the engine (i.e. nm for GROMACS). We just have not gone through all the examples yet.

As you probably guessed, the example was written with NAMD and LAMMPS in mind. Until we correct it for GROMACS, please assume nm.

Thanks
Giacomo