Re: [gmx-users] Thin film drifting
Den 2020-03-29 kl. 22:46, skrev Alex: On Sun, Mar 29, 2020 at 2:49 PM David van der Spoel 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 Note that the net movement is a lot smaller than the fluctuations in the in the one with PBC, I don't think there is any problem. 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. I would go for comm-grps = system. Make sure to compute the pmf based on the relative distance between your compound and the membrane. 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
Re: [gmx-users] Thin film drifting
On Sun, Mar 29, 2020 at 2:49 PM David van der Spoel 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? > >
Re: [gmx-users] Thin film drifting
Den 2020-03-29 kl. 19:43, skrev Alex: Thanks. On Sun, Mar 29, 2020 at 11:59 AM David van der Spoel 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. 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. 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.,
Re: [gmx-users] Thin film drifting
Thanks. On Sun, Mar 29, 2020 at 11:59 AM David van der Spoel 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
Re: [gmx-users] Thin film drifting
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 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.
Re: [gmx-users] Thin film drifting
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. Best regards, Alex On Sun, Mar 29, 2020 at 2:44 AM David van der Spoel 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. > -- 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.
Re: [gmx-users] Thin film drifting
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.
[gmx-users] Thin film drifting
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 -- 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.
