Bond constraints for annealing - protein in membrane

User discussions
1

GROMACS version: gromacs-2022.4
GROMACS modification: No
Hello,
I want to run a simulation of a protein in membrane, which I prepared using CHARMM GUI membrane builder. When I set the simulation for the annealing, I got the following note

NOTE 3 [file topol.top, line 30]:
*** The bond in molecule-type PROA between atoms 9 OG1 and 10 HG1 has an***
*** estimated oscillational period of 9.1e-03 ps, which is less than 10 times***
*** the time step of 1.0e-03 ps.***
*** Maybe you forgot to change the constraints mdp option.***

The bond constraints were set to none. Is this how is best to be for annealing or do I change it to all bonds? I searched and read that mdp files should not have constraints at none but it is unclear to me if this applies to annealing as well (and couldn’t find any answer in the annealing section in the documentations).

Could you please advice on what’s best to do?

Thanks in advance.
Dimitris

2

Hi,
Use of bond constraints and the value of time step depend on the force field that you use and how it was parameterized. For example for several biomolecular force fields, the option constraints=h-bonds has to be set in the mdp file.
I suggest to check which setting is the setting for the force field you use.
Best regards
Alessandra

3

Hi Alessandra,
Thank you so much for your time and reply, greatly appreciated.
OK, will do that. I tend to remember it was h-bonds as you said but will double check.
All the best,
Dimitris