On Sun, Mar 29, 2020 at 2:49 PM David van der Spoel <sp...@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 < > sp...@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 < > >> 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 > >>>> -- > >>>> Gromacs Users mailing list > >>>> > >>>> * Please search the archive at > >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >>>> posting! > >>>> > >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>>> > >>>> * For (un)subscribe requests visit > >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >>>> send a mail to gmx-users-requ...@gromacs.org. > >>>> > >> > >> > >> -- > >> 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! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-requ...@gromacs.org. > >> > > > -- > 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! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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