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deGrootLab / pmx

Toolkit for free-energy calculation setup/analysis and biomolecular structure handling
GNU Lesser General Public License v3.0
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Repartitioning dummy atom hydrogen mass #45

Open DreamCykl opened 8 months ago

DreamCykl commented 8 months ago

Hi, I've been using PMX for a while now and a thought has just popped in to my head: I'm repartitioning hydrogen mass with a scale factor of 3, but noticed in my top files that the dummy atoms added will not be scaled. I.e. I will have hydrogens that are non-dummy with a mass of 3, but the dummy hydrogen atoms will have a mass of 1. Does it matter if the dummy atoms that are being transitioned into /away from are not the same mass as the non-dummy atoms?

I feel like this shouldn't be an issue but I wanted to check just incase,

Thanks.

pbuslaev commented 3 months ago

You don't need to repartition atoms manually. In GROMACS2024 there is a mdp option for repartitioning at the grompp step

vgapsys commented 3 months ago

That is a useful tip @pbuslaev Do you know if it repartitions states A and B independently?

pbuslaev commented 3 months ago

I think it is not supported (and I think for a good reason) with mass differences but mass B is also repartitioned