[gmx-users] Thin film drifting

[Alex]

Thanks.

On Sun, Mar 29, 2020 at 11:59 AM David van der Spoel <spoel at xray.bmc.uu.se>
wrote:

> 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?
>
Yes, the pcoupltype is isotropic. Please find the mdp file in below link.
https://drive.google.com/open?id=1iYt6eTcQ4SBi1A9ZFOenL7Q7wc37UvLa

>
> Is the shift towards higher x and y values?
>
The shift is toward higher y value (+y).
It also firstly goes toward higher x value (+x ) for a very short time and
then switches the direction to toward lower x value (-x) and finally shifts
toward lower x value (-x).

Maybe you can open an issue here:
> https://gitlab.com/gromacs/gromacs/-/issues

I will open an issue.

Actually, in the later steps of the simulations, using umbrella sampling
and wham, I want to simulate the PMF a single molecule (called A; 26 atoms)
when it comes from water and diffuses inside the thin film till mid (com)
of thin film. pull_group1 and pull_group2 would be the Mol_A and thin_film,
respectively.

I don't know if this kind of drifting would affect on the PMF, if so, how?
If the comm-grps works I have the two following options to consider:
“comm-grps = thin_film Mol_A SOL”
or
“comm-grps = Other SOL”
Where the Other group contains the thin film and molecule A.
Which one do you recommend, please?

Thank you,
Alex

>
> >
> > 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
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