[gmx-users] Thin film drifting

[Alex]

On Sun, Mar 29, 2020 at 2:49 PM David van der Spoel <spoel at xray.bmc.uu.se>
wrote:

> Den 2020-03-29 kl. 19:43, skrev 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).
> >
> But how is the solid modeled? Are there covalent bonds? It is not
> certain there is a problem, at least I am not convinced. In P scaling
> the coordinates of all particles are scaled by a constant and then
> certain atoms can hop over PBC. If you plot the center of mass including
> periodic boundaries (i.e. without unwrapping) it will be nicely in the
> center of the box with few fluctuations. gmx traj may do this for you.
>
The thin film contains 1075 epoxy molecules in which there is no
inter-molecule covalent bond.
Below are the COM of the thin film with and without pbc in gmx traj.

I admit you are right and the comm-grps works fine as gmx traj -pbc yes
shows, thanks.
PBC : Yes
https://drive.google.com/open?id=14DRIZVt99x8SfO6qlkhPAeTkb7RQhsUp

PBC: No
https://drive.google.com/open?id=1uWRgTATW9hUEOaQQnQozklUvux8psrPx

>
> I and many others have done PMFs of small compounds over membranes of
> different types, but not sure that anyone has noticed problems with
> moving membranes.

I would also be so appreciated if you give me your preferences of the
following two choices I have in the PMF calculation of Mol_A to the
thin-film.
“comm-grps = *thin_film* *Mol_A* *SOL*”
or
“comm-grps = *Other* *SOL*”
Where the Other group contains the thin film and molecule A.

Best regards,
Alex

>
>
> > 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
> >>>> --
> >>>> Gromacs Users mailing list
> >>>>
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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
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
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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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