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

[Jochen Hub]

Hi Bert,

thanks for this quick suggestion. I just tried with the latest 
release-2021 from gitlab (2021.1-dev-20210219-d8cd16f885-unknown) and it 
did not help.

Apparently, if I got this right, the fix you mentioned affects only the 
dH/dl calculations and should not change the simulation trajectory. Our 
issue affect the trajectory massively, as the box expands within 
picoseconds.

Cheers,
Jochen


Am 02.03.21 um 09:41 schrieb Bert de Groot:
> Hi Jochen,
> 
> sounds as if this could be related to 
> https://gitlab.com/gromacs/gromacs/-/issues/3943
> 
> which was fixed only very recently:
> 
> https://gitlab.com/gromacs/gromacs/-/merge_requests/1197
> 
> could you perhaps test if that fixes your issue as well?
> 
> cheers
> 
> Bert
> 
> 
> 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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Prof. Dr. Jochen Hub
Theoretical Biophysics Group
Department of Physics, Saarland University
Campus E2 6, Zi. 4.11, 66123 Saarbruecken, Germany
Phone: +49 (0)681 302-2740
https://biophys.uni-saarland.de/
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