[gmx-users] Thin film drifting

[David van der Spoel]

Den 2020-03-29 kl. 15:16, skrev Alex:
> Thank Prof. van der Spoel for the response.
> No, it isn't. The thin film is solid. There are interaction within the thin
> film and with water in the interface.
> 
> Please find a short movie of the unwrapped trajectory of the simulation in
> below link (water molecules are hidden); It shows minimization, then
> equalization (NVT : tcoupl = v-rescale), then equalization (NpT : tcoupl =
> v-rescale and pcoupl = berendsen) and then production (NpT : tcoupl =
> v-rescale and pcoupl = Parrinello-Rahman).
> 
> https://drive.google.com/open?id=1jk-Pun1BICNArGJaW0ydIY5TTivECGMf
> 
> The thin film starts drifting significantly in the production along both x
> and y directions.
Thanks, do you have isotropic pressure scaling?

Is the shift towards higher x and y values?

Maybe you can open an issue here:
https://gitlab.com/gromacs/gromacs/-/issues
> 
> Best regards,
> Alex
> 
> On Sun, Mar 29, 2020 at 2:44 AM David van der Spoel <spoel at xray.bmc.uu.se>
> wrote:
> 
>> Den 2020-03-29 kl. 05:24, skrev Alex:
>>> Dear all,
>>> In a system, I have a thin_film (infinitive in x-y directions) with water
>>> on top and bottom of it, PBC = xyz.
>>> By the below flags I try to remove the motion of the center of mass of
>> the
>>> two group separately.
>>> comm-grps     = thin_film Water
>>> comm-mode   = Linear
>>> nstcomm         = 100
>>>
>>> However the thin film drift specially in x and y directions whereas I was
>>> expecting to have no drifting for the thin film, If I understood
>> correctly
>>> the usage of the comm-grps!
>>>
>>> Would you please let me know how I can stop drifting of the thin film?
>>>
>>> Thank you,
>>> Alex
>>>
>> Is that a liquid film? Are there interactions within the film and with
>> water? The comm removal will calculate the center of mass taking
>> periodic boundaries into account so if your film moves one molecule at a
>> time the COM will stay in place. In a realistic system the friction
>> between water and film should prevent this, hav eyou tried turning off
>> comm?
>>
>> Historically this has been a fix for the Berendsen thermostat that
>> accumulates energy, however with a stochastic thermostat it should not
>> be necessary. Not sure about Nose-Hoover though.
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Head of Department, Cell & Molecular Biology, Uppsala University.
>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
>> http://www.icm.uu.se
>> --
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-- 
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se