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 <sp...@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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http://www.icm.uu.se
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