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). 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. > -- 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.