Bond type 6 and constraints=all-bonds

User discussions
1

GROMACS version: 2019+
GROMACS modification: No

Hi,

According to the manual, distance restraints in a molecule can be created with a bond of type 6 (or type 10 for upper and lower limits). I wonder how these bond types interplay with constraints=all-bonds. The manual states, that this setting converts all bonds to constraints, but it’s unclear to me if this only affects “true” chemical bonds (bond type 1,5,7,8) or all of them. More concrete: Will bonds of type 6 still be flexible with the constrained bonds setting or are they also converted to constraints?

Thanks in advance!

Daniel

2

Bonds of type 6 should not be converted. You can verify this without even having to run the simulation by using gmx dump on the .tpr file and confirming the interaction type.

3

Thanks for your answer. (And also the hint to use gmx dump for that)

Problem solved! :)