[gmx-developers] Incorrectly large pressures at lambda=1 with perturbed masses
paul.bauer.q at gmail.com
Tue Mar 2 10:17:31 CET 2021
I'll have a look at this now and see if I can bisect this to the
Can you please open an issue on GitLab for this as well and include the
test system there?
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.
> Am 02.03.21 um 09:41 schrieb Bert de Groot:
>> 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:
>>> (The relaxation in the problematic cases is due to rapid box
>>> We have a test system here:
>>> 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
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