GROMACS version: 2020.6
GROMACS modification: No
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Actually I am confused in taking what constraint parameter i.e“constraints = all-bonds” or “constraints = h-bonds” will be suitable for nvt and npt production run. Is there any documentation or link from where I can understand the details.
Thanks in advance
this typically depends on how the force field you are using was parametrized: I’d keep it that way as the FF recommends. The MDP option you are looking for is documented here (with the others):
In short, if you use ‘h-bonds’, bonds between hydrogens and heavy atoms will be treated as rigid rods, instead of harmonic oscillators. ‘all-bonds’ makes all bonds (i.e. between heavy atoms, too) behave as rigid rods.
Hope that helps,
Thanks for the response. It helped me to understand.