Unknown left-hand 'mass-repartitioning-factor' in parameter file

User discussions
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1

GROMACS version: 2024-1
GROMACS modification: No
Hi,
I am trying to run gromacs v2024-1 with hydrogen mass repartitioning to allow a 4fs time step. The manual for this version mentions parameter ‘mass-repartitioning-factor’ for this purpose. When trying to generate the tpr file with this keyword, I get the warning:

WARNING 1 [file md.mdp, line 58]:
Unknown left-hand ‘mass-repartitioning-factor’ in parameter file

Is this keyword perhaps deprecated and completely replaced by pdb2gmx parameter -heavyh? In this case, I also have a ligand in my system which I prepared with antechamber. is HMR compatible at all with this system then (the mass of the hydrogens in the ligand topology is 1)?
Thanks!

2

Hi!

That’s a typo in the manual. The correct parameter name is mass-repartition-factor.

The manual will be fixed in GROMACS 2024.2.

3

Hi,

Thanks for the quick response. Working perfectly with this adjustment!