Re: [gmx-users] Artifact in pull-pbc-ref-prev-step-com
Hi, On 2020-04-24 20:32, Alex wrote: Hi Magnus, I see, many thanks for the insights. On Thu, Apr 23, 2020 at 2:45 AM Magnus Lundborg < magnus.lundb...@scilifelab.se> wrote: Hi Alex, pull-group1-pbcatom lets you specify the exact atom used as the PBC reference. Both 0 and -1 are special cases. For small molecules 0 is (almost?) always OK. Find one in the center of you membrane (in the pull direction). I'll actually have to check if -1 is even compatible with pull-pbc-ref-prev-step-com. It's possible that that combination should not be allowed even. So, the pull-group1-pbcatm could be any other number as atom number rather than 0 and -1. Yes, pick an atom located centrally in the structure. As you say, you can define a subgroup within the larger membrane group, but that is mainly of use if you know that some atoms consistently in the center of the whole group and others are more flexible. In this case where the subgroup defined in index.ndx file has more than one atom e.g. 30 atoms, which one of the atom in subgroup should be assigned to the pull-group1-pbcatom? If I am not mistaken, here, the entry number in index.ndx file belong to the subgroup should be assigned to the pull-group1-pbcatom. [ system ] [ Other ] [ non-water ] [ subgroup ] Would you please confirm if I am correct? Yes, pick one atom from that subgroup, the atom should be centrally placed (at least not so far away that the COM of the pull group could be wrongly calculated). In almost all cases any atom should work (and in those cases using '0' should work as well, but makes it less transparent regarding what atom is used). With "pull-pbc-ref-prev-step-com" the specified atom is only used to set the PBC initially. After that the COM of the previous step is used, making it less sensitive if the chosen atom is very mobile. Cheers, Magnus Thank you Alex Regards, Magnus On 2020-04-21 16:24, Alex wrote: Hi Magnus, Actually I am confused with the available options for the "pull-pbc-ref-prev-step-com" and "pull-group1-pbcatom". For pull-pbc-ref-prev-step-com : YES or NO: where YES should be used when one of the group is large, even the 2020.1 version of grmacs would give a warning if one used No in a case of presence of a large group. Also, for the pull-group1-pbcatom: there are two options of 0 or -1. By 0 the middle atom (number wise) of the large group is used automatically which is safe only for small groups as manual states. So, only remaining option is -1. So, what I understood for a layered-large group similar to what I have one should use pull-pbc-ref-prev-step-com = YES and pull-group1-pbcatom = -1 which would cause moving the system along -Z during the pulling. Using gmx select, can I manually define a sub-group around the COM of the large group, and consider it as one of the pulling groups instead of the large group? Thank you Alex On Mon, Apr 20, 2020 at 8:46 AM Magnus Lundborg < magnus.lundb...@scilifelab.se> wrote: Hi Alex, I don't see why it would need pull-group1-pbcatom = -1. Why not pick a central atom? Regards, Magnus On 2020-04-20 13:40, Alex wrote: Hi Magnus, Thanks. The problem raises only because of using the pull-pbc-ref-prev-step-com which needs the pull-group1-pbcatom to be -1 to be meaningful. For an identical system and mdp parameters using 2018 version of gromacs which is independent to the pull-pbc-ref-prev-step-com, I see no issue. Regards, Alex On Mon, Apr 20, 2020 at 3:27 AM Magnus Lundborg < magnus.lundb...@scilifelab.se> wrote: Sorry, about the statement about pbcatom -1. I was thinking about 0. I don't know if pbcatom -1 is good or not in this case. Regards, Magnus On 2020-04-20 09:24, Magnus Lundborg wrote: Hi Alex, I don't think this is related to using pull-pbc-ref-prev-step-com. Have you tried without it? However, it is risky using pbcatom -1, since you don't know what atom you are using as the initial reference. I would suggest picking an atom you know is located at the centre of the structure. I would think that the problem has to do with the comm removal. What are your parameters for comm-mode, nstcomm and comm-grps? It is possible that you need to lower your nstcomm. It is also possible, but not certain, the comm-mode Linear-acceleration-correction might help you. For some reason, it seems like I have sometimes avoided similar problems by using the sd integrator instead, but I haven't evaluated that properly - it might just have been coincidences. If you see a clear difference using the sd integrator it might be good if you'd file an issue about it on gitlab so that someone can look into if there is something wrong. Regards, Magnus On 2020-04-18 20:12, Alex wrote: Dear all, To generate the initial configurations for umbrella sampling, I conducted a simple pulling simulation by which a single-small molecule (mol_A) is being dragged along -Z from water into the body of a thin film. Since the thin film is large I used *"pull-pbc-r
Re: [gmx-users] Artifact in pull-pbc-ref-prev-step-com
Hi Magnus, I see, many thanks for the insights. On Thu, Apr 23, 2020 at 2:45 AM Magnus Lundborg < magnus.lundb...@scilifelab.se> wrote: > Hi Alex, > > pull-group1-pbcatom lets you specify the exact atom used as the PBC > reference. Both 0 and -1 are special cases. For small molecules 0 is > (almost?) always OK. Find one in the center of you membrane (in the pull > direction). I'll actually have to check if -1 is even compatible with > pull-pbc-ref-prev-step-com. It's possible that that combination should > not be allowed even. > So, the pull-group1-pbcatm could be any other number as atom number rather than 0 and -1. > > As you say, you can define a subgroup within the larger membrane group, > but that is mainly of use if you know that some atoms consistently in > the center of the whole group and others are more flexible. > In this case where the subgroup defined in index.ndx file has more than one atom e.g. 30 atoms, which one of the atom in subgroup should be assigned to the pull-group1-pbcatom? If I am not mistaken, here, the entry number in index.ndx file belong to the subgroup should be assigned to the pull-group1-pbcatom. [ system ] [ Other ] [ non-water ] [ subgroup ] Would you please confirm if I am correct? Thank you Alex > Regards, > > Magnus > > On 2020-04-21 16:24, Alex wrote: > > Hi Magnus, > > Actually I am confused with the available options for the > > "pull-pbc-ref-prev-step-com" and "pull-group1-pbcatom". > > For pull-pbc-ref-prev-step-com : YES or NO: where YES should be used when > > one of the group is large, even the 2020.1 version of grmacs would give a > > warning if one used No in a case of presence of a large group. > > Also, for the pull-group1-pbcatom: there are two options of 0 or -1. By 0 > > the middle atom (number wise) of the large group is used automatically > > which is safe only for small groups as manual states. So, only > > remaining option is -1. > > So, what I understood for a layered-large group similar to what I have > one > > should use pull-pbc-ref-prev-step-com = YES and pull-group1-pbcatom = -1 > > which would cause moving the system along -Z during the pulling. > > > > Using gmx select, can I manually define a sub-group around the COM of the > > large group, and consider it as one of the pulling groups instead of the > > large group? > > > > Thank you > > Alex > > > > On Mon, Apr 20, 2020 at 8:46 AM Magnus Lundborg < > > magnus.lundb...@scilifelab.se> wrote: > > > >> Hi Alex, > >> > >> I don't see why it would need pull-group1-pbcatom = -1. Why not pick a > >> central atom? > >> > >> Regards, > >> > >> Magnus > >> > >> On 2020-04-20 13:40, Alex wrote: > >>> Hi Magnus, > >>> Thanks. > >>> The problem raises only because of using the pull-pbc-ref-prev-step-com > >>> which needs the pull-group1-pbcatom to be -1 to be meaningful. > >>> For an identical system and mdp parameters using 2018 version of > gromacs > >>> which is independent to the pull-pbc-ref-prev-step-com, I see no issue. > >>> > >>> Regards, > >>> Alex > >>> > >>> On Mon, Apr 20, 2020 at 3:27 AM Magnus Lundborg < > >>> magnus.lundb...@scilifelab.se> wrote: > >>> > Sorry, about the statement about pbcatom -1. I was thinking about 0. I > don't know if pbcatom -1 is good or not in this case. > > Regards, > > Magnus > > On 2020-04-20 09:24, Magnus Lundborg wrote: > > Hi Alex, > > > > I don't think this is related to using pull-pbc-ref-prev-step-com. > > Have you tried without it? However, it is risky using pbcatom -1, > > since you don't know what atom you are using as the initial > reference. > > I would suggest picking an atom you know is located at the centre of > > the structure. > > > > I would think that the problem has to do with the comm removal. What > > are your parameters for comm-mode, nstcomm and comm-grps? It is > > possible that you need to lower your nstcomm. It is also possible, > but > > not certain, the comm-mode Linear-acceleration-correction might help > > you. For some reason, it seems like I have sometimes avoided similar > > problems by using the sd integrator instead, but I haven't evaluated > > that properly - it might just have been coincidences. If you see a > > clear difference using the sd integrator it might be good if you'd > > file an issue about it on gitlab so that someone can look into if > > there is something wrong. > > > > Regards, > > Magnus > > > > On 2020-04-18 20:12, Alex wrote: > >> Dear all, > >> To generate the initial configurations for umbrella sampling, I > >> conducted a > >> simple pulling simulation by which a single-small molecule (mol_A) > is > >> being > >> dragged along -Z from water into the body of a thin film. > >> Since the thin film is large I used *"pull-pbc-ref-prev-step-com = > >> yes" and > >> "pull-group1-pbcatom = -1"* which cause a net shifting of
Re: [gmx-users] Artifact in pull-pbc-ref-prev-step-com
Hi Alex, pull-group1-pbcatom lets you specify the exact atom used as the PBC reference. Both 0 and -1 are special cases. For small molecules 0 is (almost?) always OK. Find one in the center of you membrane (in the pull direction). I'll actually have to check if -1 is even compatible with pull-pbc-ref-prev-step-com. It's possible that that combination should not be allowed even. As you say, you can define a subgroup within the larger membrane group, but that is mainly of use if you know that some atoms consistently in the center of the whole group and others are more flexible. Regards, Magnus On 2020-04-21 16:24, Alex wrote: Hi Magnus, Actually I am confused with the available options for the "pull-pbc-ref-prev-step-com" and "pull-group1-pbcatom". For pull-pbc-ref-prev-step-com : YES or NO: where YES should be used when one of the group is large, even the 2020.1 version of grmacs would give a warning if one used No in a case of presence of a large group. Also, for the pull-group1-pbcatom: there are two options of 0 or -1. By 0 the middle atom (number wise) of the large group is used automatically which is safe only for small groups as manual states. So, only remaining option is -1. So, what I understood for a layered-large group similar to what I have one should use pull-pbc-ref-prev-step-com = YES and pull-group1-pbcatom = -1 which would cause moving the system along -Z during the pulling. Using gmx select, can I manually define a sub-group around the COM of the large group, and consider it as one of the pulling groups instead of the large group? Thank you Alex On Mon, Apr 20, 2020 at 8:46 AM Magnus Lundborg < magnus.lundb...@scilifelab.se> wrote: Hi Alex, I don't see why it would need pull-group1-pbcatom = -1. Why not pick a central atom? Regards, Magnus On 2020-04-20 13:40, Alex wrote: Hi Magnus, Thanks. The problem raises only because of using the pull-pbc-ref-prev-step-com which needs the pull-group1-pbcatom to be -1 to be meaningful. For an identical system and mdp parameters using 2018 version of gromacs which is independent to the pull-pbc-ref-prev-step-com, I see no issue. Regards, Alex On Mon, Apr 20, 2020 at 3:27 AM Magnus Lundborg < magnus.lundb...@scilifelab.se> wrote: Sorry, about the statement about pbcatom -1. I was thinking about 0. I don't know if pbcatom -1 is good or not in this case. Regards, Magnus On 2020-04-20 09:24, Magnus Lundborg wrote: Hi Alex, I don't think this is related to using pull-pbc-ref-prev-step-com. Have you tried without it? However, it is risky using pbcatom -1, since you don't know what atom you are using as the initial reference. I would suggest picking an atom you know is located at the centre of the structure. I would think that the problem has to do with the comm removal. What are your parameters for comm-mode, nstcomm and comm-grps? It is possible that you need to lower your nstcomm. It is also possible, but not certain, the comm-mode Linear-acceleration-correction might help you. For some reason, it seems like I have sometimes avoided similar problems by using the sd integrator instead, but I haven't evaluated that properly - it might just have been coincidences. If you see a clear difference using the sd integrator it might be good if you'd file an issue about it on gitlab so that someone can look into if there is something wrong. Regards, Magnus On 2020-04-18 20:12, Alex wrote: Dear all, To generate the initial configurations for umbrella sampling, I conducted a simple pulling simulation by which a single-small molecule (mol_A) is being dragged along -Z from water into the body of a thin film. Since the thin film is large I used *"pull-pbc-ref-prev-step-com = yes" and "pull-group1-pbcatom = -1"* which cause a net shifting of the system along the pulling direction as soon as the mol_A reach to the thin film, please find below the pulling flags movie and plot in below links. Centering the thin film and mol_A could solve the issue, (echo 1 0 | trjconv -center yes) to some extent but still COM changes in the early stage below 2ns. , COM: https://drive.google.com/open?id=1-EcnV1uSu0I3eqdvjuUf2OxTZEXFD5m0 Movie in which the water molecules are hidden: https://drive.google.com/open?id=1gP5GBgfGYMithrA1o1T_RzlSdCS91gkv - gmx version 2020.1 - pull = yes pull-print-com = no pull-print-ref-value = yes pull-print-components= Yes pull-nstxout = 1000 pull-nstfout = 1000 pull-pbc-ref-prev-step-com = yes pull-ngroups = 2 pull-ncoords = 1 pull-group1-name = Thin-film pull-group1-pbcatom = -1 pull-group2-name = mol_A pull-group2-pbcatom = 0 pull-coord1-type = umbrella pull-coord1-geometry = direction pull-coord1-groups = 1 2 pull-coord1-dim = N N Y pull-coord1-origin = 0.0 0.0 0.0 pull-coord1-vec = 0.0 0.0 -1.0 pull-coord1-start= yes pull-coord1-init =
Re: [gmx-users] Artifact in pull-pbc-ref-prev-step-com
Hi Magnus, Actually I am confused with the available options for the "pull-pbc-ref-prev-step-com" and "pull-group1-pbcatom". For pull-pbc-ref-prev-step-com : YES or NO: where YES should be used when one of the group is large, even the 2020.1 version of grmacs would give a warning if one used No in a case of presence of a large group. Also, for the pull-group1-pbcatom: there are two options of 0 or -1. By 0 the middle atom (number wise) of the large group is used automatically which is safe only for small groups as manual states. So, only remaining option is -1. So, what I understood for a layered-large group similar to what I have one should use pull-pbc-ref-prev-step-com = YES and pull-group1-pbcatom = -1 which would cause moving the system along -Z during the pulling. Using gmx select, can I manually define a sub-group around the COM of the large group, and consider it as one of the pulling groups instead of the large group? Thank you Alex On Mon, Apr 20, 2020 at 8:46 AM Magnus Lundborg < magnus.lundb...@scilifelab.se> wrote: > Hi Alex, > > I don't see why it would need pull-group1-pbcatom = -1. Why not pick a > central atom? > > Regards, > > Magnus > > On 2020-04-20 13:40, Alex wrote: > > Hi Magnus, > > Thanks. > > The problem raises only because of using the pull-pbc-ref-prev-step-com > > which needs the pull-group1-pbcatom to be -1 to be meaningful. > > For an identical system and mdp parameters using 2018 version of gromacs > > which is independent to the pull-pbc-ref-prev-step-com, I see no issue. > > > > Regards, > > Alex > > > > On Mon, Apr 20, 2020 at 3:27 AM Magnus Lundborg < > > magnus.lundb...@scilifelab.se> wrote: > > > >> Sorry, about the statement about pbcatom -1. I was thinking about 0. I > >> don't know if pbcatom -1 is good or not in this case. > >> > >> Regards, > >> > >> Magnus > >> > >> On 2020-04-20 09:24, Magnus Lundborg wrote: > >>> Hi Alex, > >>> > >>> I don't think this is related to using pull-pbc-ref-prev-step-com. > >>> Have you tried without it? However, it is risky using pbcatom -1, > >>> since you don't know what atom you are using as the initial reference. > >>> I would suggest picking an atom you know is located at the centre of > >>> the structure. > >>> > >>> I would think that the problem has to do with the comm removal. What > >>> are your parameters for comm-mode, nstcomm and comm-grps? It is > >>> possible that you need to lower your nstcomm. It is also possible, but > >>> not certain, the comm-mode Linear-acceleration-correction might help > >>> you. For some reason, it seems like I have sometimes avoided similar > >>> problems by using the sd integrator instead, but I haven't evaluated > >>> that properly - it might just have been coincidences. If you see a > >>> clear difference using the sd integrator it might be good if you'd > >>> file an issue about it on gitlab so that someone can look into if > >>> there is something wrong. > >>> > >>> Regards, > >>> Magnus > >>> > >>> On 2020-04-18 20:12, Alex wrote: > Dear all, > To generate the initial configurations for umbrella sampling, I > conducted a > simple pulling simulation by which a single-small molecule (mol_A) is > being > dragged along -Z from water into the body of a thin film. > Since the thin film is large I used *"pull-pbc-ref-prev-step-com = > yes" and > "pull-group1-pbcatom = -1"* which cause a net shifting of the > system > along the pulling direction as soon as the mol_A reach to the thin > film, > please find below the pulling flags movie and plot in below links. > > Centering the thin film and mol_A could solve the issue, (echo 1 0 | > trjconv -center yes) to some extent but still COM changes in the early > stage below 2ns. , > COM: > https://drive.google.com/open?id=1-EcnV1uSu0I3eqdvjuUf2OxTZEXFD5m0 > > Movie in which the water molecules are hidden: > https://drive.google.com/open?id=1gP5GBgfGYMithrA1o1T_RzlSdCS91gkv > > - > gmx version 2020.1 > - > pull = yes > pull-print-com = no > pull-print-ref-value = yes > pull-print-components= Yes > pull-nstxout = 1000 > pull-nstfout = 1000 > pull-pbc-ref-prev-step-com = yes > pull-ngroups = 2 > pull-ncoords = 1 > pull-group1-name = Thin-film > pull-group1-pbcatom = -1 > pull-group2-name = mol_A > pull-group2-pbcatom = 0 > pull-coord1-type = umbrella > pull-coord1-geometry = direction > pull-coord1-groups = 1 2 > pull-coord1-dim = N N Y > pull-coord1-origin = 0.0 0.0 0.0 > pull-coord1-vec = 0.0 0.0 -1.0 > pull-coord1-start= yes > pull-coord1-init = 0 > pull-coord1-rate = 0.0005 > pull-coord1-k= 5000 > - > >
Re: [gmx-users] Artifact in pull-pbc-ref-prev-step-com
Hi Alex, I don't see why it would need pull-group1-pbcatom = -1. Why not pick a central atom? Regards, Magnus On 2020-04-20 13:40, Alex wrote: Hi Magnus, Thanks. The problem raises only because of using the pull-pbc-ref-prev-step-com which needs the pull-group1-pbcatom to be -1 to be meaningful. For an identical system and mdp parameters using 2018 version of gromacs which is independent to the pull-pbc-ref-prev-step-com, I see no issue. Regards, Alex On Mon, Apr 20, 2020 at 3:27 AM Magnus Lundborg < magnus.lundb...@scilifelab.se> wrote: Sorry, about the statement about pbcatom -1. I was thinking about 0. I don't know if pbcatom -1 is good or not in this case. Regards, Magnus On 2020-04-20 09:24, Magnus Lundborg wrote: Hi Alex, I don't think this is related to using pull-pbc-ref-prev-step-com. Have you tried without it? However, it is risky using pbcatom -1, since you don't know what atom you are using as the initial reference. I would suggest picking an atom you know is located at the centre of the structure. I would think that the problem has to do with the comm removal. What are your parameters for comm-mode, nstcomm and comm-grps? It is possible that you need to lower your nstcomm. It is also possible, but not certain, the comm-mode Linear-acceleration-correction might help you. For some reason, it seems like I have sometimes avoided similar problems by using the sd integrator instead, but I haven't evaluated that properly - it might just have been coincidences. If you see a clear difference using the sd integrator it might be good if you'd file an issue about it on gitlab so that someone can look into if there is something wrong. Regards, Magnus On 2020-04-18 20:12, Alex wrote: Dear all, To generate the initial configurations for umbrella sampling, I conducted a simple pulling simulation by which a single-small molecule (mol_A) is being dragged along -Z from water into the body of a thin film. Since the thin film is large I used *"pull-pbc-ref-prev-step-com = yes" and "pull-group1-pbcatom = -1"* which cause a net shifting of the system along the pulling direction as soon as the mol_A reach to the thin film, please find below the pulling flags movie and plot in below links. Centering the thin film and mol_A could solve the issue, (echo 1 0 | trjconv -center yes) to some extent but still COM changes in the early stage below 2ns. , COM: https://drive.google.com/open?id=1-EcnV1uSu0I3eqdvjuUf2OxTZEXFD5m0 Movie in which the water molecules are hidden: https://drive.google.com/open?id=1gP5GBgfGYMithrA1o1T_RzlSdCS91gkv - gmx version 2020.1 - pull = yes pull-print-com = no pull-print-ref-value = yes pull-print-components= Yes pull-nstxout = 1000 pull-nstfout = 1000 pull-pbc-ref-prev-step-com = yes pull-ngroups = 2 pull-ncoords = 1 pull-group1-name = Thin-film pull-group1-pbcatom = -1 pull-group2-name = mol_A pull-group2-pbcatom = 0 pull-coord1-type = umbrella pull-coord1-geometry = direction pull-coord1-groups = 1 2 pull-coord1-dim = N N Y pull-coord1-origin = 0.0 0.0 0.0 pull-coord1-vec = 0.0 0.0 -1.0 pull-coord1-start= yes pull-coord1-init = 0 pull-coord1-rate = 0.0005 pull-coord1-k= 5000 - I wonder if I could extract correct initial configuration from this trajectory? With correct initial configuration, I mean a set of gro file in which change from one from to another is the distance between the COM of the thin-film and mol_A? 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. -- 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] Artifact in pull-pbc-ref-prev-step-com
Hi Magnus, Thanks. The problem raises only because of using the pull-pbc-ref-prev-step-com which needs the pull-group1-pbcatom to be -1 to be meaningful. For an identical system and mdp parameters using 2018 version of gromacs which is independent to the pull-pbc-ref-prev-step-com, I see no issue. Regards, Alex On Mon, Apr 20, 2020 at 3:27 AM Magnus Lundborg < magnus.lundb...@scilifelab.se> wrote: > Sorry, about the statement about pbcatom -1. I was thinking about 0. I > don't know if pbcatom -1 is good or not in this case. > > Regards, > > Magnus > > On 2020-04-20 09:24, Magnus Lundborg wrote: > > Hi Alex, > > > > I don't think this is related to using pull-pbc-ref-prev-step-com. > > Have you tried without it? However, it is risky using pbcatom -1, > > since you don't know what atom you are using as the initial reference. > > I would suggest picking an atom you know is located at the centre of > > the structure. > > > > I would think that the problem has to do with the comm removal. What > > are your parameters for comm-mode, nstcomm and comm-grps? It is > > possible that you need to lower your nstcomm. It is also possible, but > > not certain, the comm-mode Linear-acceleration-correction might help > > you. For some reason, it seems like I have sometimes avoided similar > > problems by using the sd integrator instead, but I haven't evaluated > > that properly - it might just have been coincidences. If you see a > > clear difference using the sd integrator it might be good if you'd > > file an issue about it on gitlab so that someone can look into if > > there is something wrong. > > > > Regards, > > Magnus > > > > On 2020-04-18 20:12, Alex wrote: > >> Dear all, > >> To generate the initial configurations for umbrella sampling, I > >> conducted a > >> simple pulling simulation by which a single-small molecule (mol_A) is > >> being > >> dragged along -Z from water into the body of a thin film. > >> Since the thin film is large I used *"pull-pbc-ref-prev-step-com = > >> yes" and > >> "pull-group1-pbcatom = -1"* which cause a net shifting of the > >> system > >> along the pulling direction as soon as the mol_A reach to the thin film, > >> please find below the pulling flags movie and plot in below links. > >> > >> Centering the thin film and mol_A could solve the issue, (echo 1 0 | > >> trjconv -center yes) to some extent but still COM changes in the early > >> stage below 2ns. , > >> COM: > >> https://drive.google.com/open?id=1-EcnV1uSu0I3eqdvjuUf2OxTZEXFD5m0 > >> > >> Movie in which the water molecules are hidden: > >> https://drive.google.com/open?id=1gP5GBgfGYMithrA1o1T_RzlSdCS91gkv > >> > >> - > >> gmx version 2020.1 > >> - > >> pull = yes > >> pull-print-com = no > >> pull-print-ref-value = yes > >> pull-print-components= Yes > >> pull-nstxout = 1000 > >> pull-nstfout = 1000 > >> pull-pbc-ref-prev-step-com = yes > >> pull-ngroups = 2 > >> pull-ncoords = 1 > >> pull-group1-name = Thin-film > >> pull-group1-pbcatom = -1 > >> pull-group2-name = mol_A > >> pull-group2-pbcatom = 0 > >> pull-coord1-type = umbrella > >> pull-coord1-geometry = direction > >> pull-coord1-groups = 1 2 > >> pull-coord1-dim = N N Y > >> pull-coord1-origin = 0.0 0.0 0.0 > >> pull-coord1-vec = 0.0 0.0 -1.0 > >> pull-coord1-start= yes > >> pull-coord1-init = 0 > >> pull-coord1-rate = 0.0005 > >> pull-coord1-k= 5000 > >> - > >> I wonder if I could extract correct initial configuration from this > >> trajectory? With correct initial configuration, I mean a set of gro > >> file in > >> which change from one from to another is the distance between the COM of > >> the thin-film and mol_A? > >> > >> 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. -- 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] Artifact in pull-pbc-ref-prev-step-com
Sorry, about the statement about pbcatom -1. I was thinking about 0. I don't know if pbcatom -1 is good or not in this case. Regards, Magnus On 2020-04-20 09:24, Magnus Lundborg wrote: Hi Alex, I don't think this is related to using pull-pbc-ref-prev-step-com. Have you tried without it? However, it is risky using pbcatom -1, since you don't know what atom you are using as the initial reference. I would suggest picking an atom you know is located at the centre of the structure. I would think that the problem has to do with the comm removal. What are your parameters for comm-mode, nstcomm and comm-grps? It is possible that you need to lower your nstcomm. It is also possible, but not certain, the comm-mode Linear-acceleration-correction might help you. For some reason, it seems like I have sometimes avoided similar problems by using the sd integrator instead, but I haven't evaluated that properly - it might just have been coincidences. If you see a clear difference using the sd integrator it might be good if you'd file an issue about it on gitlab so that someone can look into if there is something wrong. Regards, Magnus On 2020-04-18 20:12, Alex wrote: Dear all, To generate the initial configurations for umbrella sampling, I conducted a simple pulling simulation by which a single-small molecule (mol_A) is being dragged along -Z from water into the body of a thin film. Since the thin film is large I used *"pull-pbc-ref-prev-step-com = yes" and "pull-group1-pbcatom = -1"* which cause a net shifting of the system along the pulling direction as soon as the mol_A reach to the thin film, please find below the pulling flags movie and plot in below links. Centering the thin film and mol_A could solve the issue, (echo 1 0 | trjconv -center yes) to some extent but still COM changes in the early stage below 2ns. , COM: https://drive.google.com/open?id=1-EcnV1uSu0I3eqdvjuUf2OxTZEXFD5m0 Movie in which the water molecules are hidden: https://drive.google.com/open?id=1gP5GBgfGYMithrA1o1T_RzlSdCS91gkv - gmx version 2020.1 - pull = yes pull-print-com = no pull-print-ref-value = yes pull-print-components = Yes pull-nstxout = 1000 pull-nstfout = 1000 pull-pbc-ref-prev-step-com = yes pull-ngroups = 2 pull-ncoords = 1 pull-group1-name = Thin-film pull-group1-pbcatom = -1 pull-group2-name = mol_A pull-group2-pbcatom = 0 pull-coord1-type = umbrella pull-coord1-geometry = direction pull-coord1-groups = 1 2 pull-coord1-dim = N N Y pull-coord1-origin = 0.0 0.0 0.0 pull-coord1-vec = 0.0 0.0 -1.0 pull-coord1-start = yes pull-coord1-init = 0 pull-coord1-rate = 0.0005 pull-coord1-k = 5000 - I wonder if I could extract correct initial configuration from this trajectory? With correct initial configuration, I mean a set of gro file in which change from one from to another is the distance between the COM of the thin-film and mol_A? 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.
Re: [gmx-users] Artifact in pull-pbc-ref-prev-step-com
Hi Alex, I don't think this is related to using pull-pbc-ref-prev-step-com. Have you tried without it? However, it is risky using pbcatom -1, since you don't know what atom you are using as the initial reference. I would suggest picking an atom you know is located at the centre of the structure. I would think that the problem has to do with the comm removal. What are your parameters for comm-mode, nstcomm and comm-grps? It is possible that you need to lower your nstcomm. It is also possible, but not certain, the comm-mode Linear-acceleration-correction might help you. For some reason, it seems like I have sometimes avoided similar problems by using the sd integrator instead, but I haven't evaluated that properly - it might just have been coincidences. If you see a clear difference using the sd integrator it might be good if you'd file an issue about it on gitlab so that someone can look into if there is something wrong. Regards, Magnus On 2020-04-18 20:12, Alex wrote: Dear all, To generate the initial configurations for umbrella sampling, I conducted a simple pulling simulation by which a single-small molecule (mol_A) is being dragged along -Z from water into the body of a thin film. Since the thin film is large I used *"pull-pbc-ref-prev-step-com = yes" and "pull-group1-pbcatom = -1"* which cause a net shifting of the system along the pulling direction as soon as the mol_A reach to the thin film, please find below the pulling flags movie and plot in below links. Centering the thin film and mol_A could solve the issue, (echo 1 0 | trjconv -center yes) to some extent but still COM changes in the early stage below 2ns. , COM: https://drive.google.com/open?id=1-EcnV1uSu0I3eqdvjuUf2OxTZEXFD5m0 Movie in which the water molecules are hidden: https://drive.google.com/open?id=1gP5GBgfGYMithrA1o1T_RzlSdCS91gkv - gmx version 2020.1 - pull = yes pull-print-com = no pull-print-ref-value = yes pull-print-components= Yes pull-nstxout = 1000 pull-nstfout = 1000 pull-pbc-ref-prev-step-com = yes pull-ngroups = 2 pull-ncoords = 1 pull-group1-name = Thin-film pull-group1-pbcatom = -1 pull-group2-name = mol_A pull-group2-pbcatom = 0 pull-coord1-type = umbrella pull-coord1-geometry = direction pull-coord1-groups = 1 2 pull-coord1-dim = N N Y pull-coord1-origin = 0.0 0.0 0.0 pull-coord1-vec = 0.0 0.0 -1.0 pull-coord1-start= yes pull-coord1-init = 0 pull-coord1-rate = 0.0005 pull-coord1-k= 5000 - I wonder if I could extract correct initial configuration from this trajectory? With correct initial configuration, I mean a set of gro file in which change from one from to another is the distance between the COM of the thin-film and mol_A? 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.
Re: [gmx-users] Artifact in pull-pbc-ref-prev-step-com
Any comment on this would be so appreciated! Regards, Alex On Sat, Apr 18, 2020 at 2:12 PM Alex wrote: > Dear all, > To generate the initial configurations for umbrella sampling, I conducted > a simple pulling simulation by which a single-small molecule (mol_A) is > being dragged along -Z from water into the body of a thin film. > Since the thin film is large I used *"pull-pbc-ref-prev-step-com = yes" > and "pull-group1-pbcatom = -1"* which cause a net shifting of the > system along the pulling direction as soon as the mol_A reach to the thin > film, please find below the pulling flags movie and plot in below links. > > Centering the thin film and mol_A could solve the issue, (echo 1 0 | > trjconv -center yes) to some extent but still COM changes in the early > stage below 2ns. , > COM: > https://drive.google.com/open?id=1-EcnV1uSu0I3eqdvjuUf2OxTZEXFD5m0 > > Movie in which the water molecules are hidden: > https://drive.google.com/open?id=1gP5GBgfGYMithrA1o1T_RzlSdCS91gkv > > - > gmx version 2020.1 > - > pull = yes > pull-print-com = no > pull-print-ref-value = yes > pull-print-components= Yes > pull-nstxout = 1000 > pull-nstfout = 1000 > pull-pbc-ref-prev-step-com = yes > pull-ngroups = 2 > pull-ncoords = 1 > pull-group1-name = Thin-film > pull-group1-pbcatom = -1 > pull-group2-name = mol_A > pull-group2-pbcatom = 0 > pull-coord1-type = umbrella > pull-coord1-geometry = direction > pull-coord1-groups = 1 2 > pull-coord1-dim = N N Y > pull-coord1-origin = 0.0 0.0 0.0 > pull-coord1-vec = 0.0 0.0 -1.0 > pull-coord1-start= yes > pull-coord1-init = 0 > pull-coord1-rate = 0.0005 > pull-coord1-k= 5000 > - > I wonder if I could extract correct initial configuration from this > trajectory? With correct initial configuration, I mean a set of gro file in > which change from one from to another is the distance between the COM of > the thin-film and mol_A? > > 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.
