[gmx-developers] Incorrectly large pressures at lambda=1 with perturbed masses

Bert de Groot bgroot at gwdg.de
Tue Mar 2 09:41:41 CET 2021

Hi Jochen,

sounds as if this could be related to 

which was fixed only very recently:


could you perhaps test if that fixes your issue as well?



On 3/2/21 9:35 AM, Jochen Hub wrote:
> Dear Gromacs developers,
> we get incorrectly large pressures in FEP simulations in the lambda=1 
> state if we perturb the masses of all hydrogen atoms. Specifically, we 
> simulate a pure-water box and perturb the masses of all H atoms from 
> 1amu to 2amu. This happens with Gromacs 2019.6, 2020.5, and 2021, but 
> NOT with 2018.6.
> The pressures are shown in a PDF here:
> https://cloud.hiz-saarland.de/s/NH6Mz8QKi39qBH7
> (The relaxation in the problematic cases is due to rapid box expansion).
> We have a test system here:
> https://cloud.hiz-saarland.de/s/o2j7K4GK7wojayi
> This does NOT happen if:
> - masses are not perturbed
> - using Gromacs 2018.6
> - the same state is defined to lambda=0 by modifying the topology
> To us, this looks like a potentially severe bug which was not detected 
> because we typically perturb only few atoms and not 2/3 of the all 
> atoms, as we do here.
> Is this issue known?
> Best wishes,
> Johanna and Jochen

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