Whether one will use hydrogen bond constraints vs all-atom bond constraints in GROMACS depends on the force field to be used.
The CHARMM36m force field is the only one in Gromacs, where constraining only hydrogen bonds is mandatory (as noted in the Gromacs manual: https://manual.gromacs.org/current/user-guide/force-fields.html).
In other force fields, both hydrogen bond constraints and full bond constraints are possible, but full bond constraints are typically chosen when the goal is to simulate longer timescales within shorter simulation durations.
If your focus is on accuracy rather than rapidly reaching long timescales, it is best to use the hydrogen bond option. This approach is also applied in DNA simulations, where the hydrogen bond option was used (https://gromacs.bioexcel.eu/t/mdp-parameters-for-non-bonded-interaction-using-the-amber-force-field/6458).
In general the option constraints=h-bonds is more compatible with other software, eg. NAMD, where particular constraints in hbond fixes https://pubs.acs.org/doi/10.1021/acs.jctc.2c00200 are used.
Ultimatitely, the choice of whether to use constraints=h-bonds or constraints=all-bonds constraints depends on how the force field is parameterized.
From here we can understand that common forcefields, including AMBER, CHARMM and OPLS/aa, are parametrized with hydrogen constrained bonds. Constraining all bonds should be avoided for correctness.
Michalis and Matilde
The CHARMM36m force field is the only one in Gromacs, where constraining only hydrogen bonds is mandatory (as noted in the Gromacs manual: https://manual.gromacs.org/current/user-guide/force-fields.html).
In other force fields, both hydrogen bond constraints and full bond constraints are possible, but full bond constraints are typically chosen when the goal is to simulate longer timescales within shorter simulation durations.
If your focus is on accuracy rather than rapidly reaching long timescales, it is best to use the hydrogen bond option. This approach is also applied in DNA simulations, where the hydrogen bond option was used (https://gromacs.bioexcel.eu/t/mdp-parameters-for-non-bonded-interaction-using-the-amber-force-field/6458).
In general the option constraints=h-bonds is more compatible with other software, eg. NAMD, where particular constraints in hbond fixes https://pubs.acs.org/doi/10.1021/acs.jctc.2c00200 are used.
Ultimatitely, the choice of whether to use constraints=h-bonds or constraints=all-bonds constraints depends on how the force field is parameterized.
From here we can understand that common forcefields, including AMBER, CHARMM and OPLS/aa, are parametrized with hydrogen constrained bonds. Constraining all bonds should be avoided for correctness.
Michalis and Matilde
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