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

[Paul bauer]

Hello Jochen,

I'll have a look at this now and see if I can bisect this to the 
breaking change.
Can you please open an issue on GitLab for this as well and include the 
test system there?

Cheers

Paul

On 02/03/2021 10:14, Jochen Hub wrote:
> 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
>>>
>>>
>>
>

-- 
Paul Bauer, PhD
GROMACS Development Manager
KTH Stockholm, SciLifeLab
0046737308594