Re: [gmx-users] Remove all but N closest water molecules from protein
Hi Mark, The following lines select solvent molecules within some cutoff distance of the protein: close_solvent_atoms = group "SOL" and within 0.5 of group "Protein"; close_solvent_molecules = same resindex as close_solvent_atoms; "strippedSystem" group "Protein" or close_solvent_molecules; It's not exactly what I wanted, butI can select N closest water molecules by tuning the cutoff distance. .Jose On Thu, Jun 8, 2017 at 4:34 AM, Mark Abraham wrote: > Hi, > > Or gmx select to make an index group for the nearest waters, and gmx > trjconv to make the subset with the index group. > > Mark > > On Thu, Jun 8, 2017 at 9:05 AM João Henriques < > joao.m.a.henriq...@gmail.com> > wrote: > > > Hi, > > > > trjorder can reorder the water molecules in each frame according to their > > distance to the protein. Then you either manually prune the gro file(s) > or > > use an index file to get rid of the extra stuff. I don't know of any > native > > tool that does all of this in one step but I may be outdated regarding > new > > stuff on gmx 2016. > > > > Cheers, > > João > > > > On Jun 8, 2017 2:49 AM, "Jose Borreguero" wrote: > > > > Dear Gromacs users, > > > > I'm a newbie with Gromacs. Is there a Gromacs native tool that will allow > > me to create a new *.gro file containing the protein and the N closest > > water molecules to the protein > > , starting from a system of a solvated protein > > ? > > > > Best, > > Jose Borreguero > > -- > > 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. > -- > 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] Remove all but N closest water molecules from protein
Thanks for the clarification. João On Thu, Jun 8, 2017 at 11:58 AM, Mark Abraham wrote: > Hi, > > No. gmx select will write index groups that could implement a dynamic > selection, but trjconv can't do anything sensible with it. You'd have to > split the trajectory into a file per frame and match the index group to the > file to get the selection into a new file. Even if trjconv was smart > enough, you'd also need to use a trajectory format and downstream tools > that were about to be flexible about the number of atoms (which is > typically not the case)... In principle, our TNG format is able to be > flexible, but there's a lot of infrastructure work if people would actually > write such files and expect to read them and have everything work well. > Better to work on tools that can use the dynamic selection without needing > to serialize and de-serialize files (and the new GROMACS analysis framework > has such support, but we don't have much funding for implementing / porting > tools to it). > > Mark > > On Thu, Jun 8, 2017 at 10:48 AM João Henriques < > joao.m.a.henriq...@gmail.com> > wrote: > > > Hi Mark, > > > > Does your solution output variable numbers of water molecules per frame? > > That is exactly what I've been wanting to do for a while, but with my > > solution it becomes very difficult to do so and I usually end up using a > > fixed number of closest waters for all frames. > > > > João > > > > > > > > On Thu, Jun 8, 2017 at 10:34 AM, Mark Abraham > > wrote: > > > > > Hi, > > > > > > Or gmx select to make an index group for the nearest waters, and gmx > > > trjconv to make the subset with the index group. > > > > > > Mark > > > > > > On Thu, Jun 8, 2017 at 9:05 AM João Henriques < > > > joao.m.a.henriq...@gmail.com> > > > wrote: > > > > > > > Hi, > > > > > > > > trjorder can reorder the water molecules in each frame according to > > their > > > > distance to the protein. Then you either manually prune the gro > file(s) > > > or > > > > use an index file to get rid of the extra stuff. I don't know of any > > > native > > > > tool that does all of this in one step but I may be outdated > regarding > > > new > > > > stuff on gmx 2016. > > > > > > > > Cheers, > > > > João > > > > > > > > On Jun 8, 2017 2:49 AM, "Jose Borreguero" > > wrote: > > > > > > > > Dear Gromacs users, > > > > > > > > I'm a newbie with Gromacs. Is there a Gromacs native tool that will > > allow > > > > me to create a new *.gro file containing the protein and the N > closest > > > > water molecules to the protein > > > > , starting from a system of a solvated protein > > > > ? > > > > > > > > Best, > > > > Jose Borreguero > > > > -- > > > > 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. > > > -- > > > 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. > -- > 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] Remove all but N closest water molecules from protein
Hi, No. gmx select will write index groups that could implement a dynamic selection, but trjconv can't do anything sensible with it. You'd have to split the trajectory into a file per frame and match the index group to the file to get the selection into a new file. Even if trjconv was smart enough, you'd also need to use a trajectory format and downstream tools that were about to be flexible about the number of atoms (which is typically not the case)... In principle, our TNG format is able to be flexible, but there's a lot of infrastructure work if people would actually write such files and expect to read them and have everything work well. Better to work on tools that can use the dynamic selection without needing to serialize and de-serialize files (and the new GROMACS analysis framework has such support, but we don't have much funding for implementing / porting tools to it). Mark On Thu, Jun 8, 2017 at 10:48 AM João Henriques wrote: > Hi Mark, > > Does your solution output variable numbers of water molecules per frame? > That is exactly what I've been wanting to do for a while, but with my > solution it becomes very difficult to do so and I usually end up using a > fixed number of closest waters for all frames. > > João > > > > On Thu, Jun 8, 2017 at 10:34 AM, Mark Abraham > wrote: > > > Hi, > > > > Or gmx select to make an index group for the nearest waters, and gmx > > trjconv to make the subset with the index group. > > > > Mark > > > > On Thu, Jun 8, 2017 at 9:05 AM João Henriques < > > joao.m.a.henriq...@gmail.com> > > wrote: > > > > > Hi, > > > > > > trjorder can reorder the water molecules in each frame according to > their > > > distance to the protein. Then you either manually prune the gro file(s) > > or > > > use an index file to get rid of the extra stuff. I don't know of any > > native > > > tool that does all of this in one step but I may be outdated regarding > > new > > > stuff on gmx 2016. > > > > > > Cheers, > > > João > > > > > > On Jun 8, 2017 2:49 AM, "Jose Borreguero" > wrote: > > > > > > Dear Gromacs users, > > > > > > I'm a newbie with Gromacs. Is there a Gromacs native tool that will > allow > > > me to create a new *.gro file containing the protein and the N closest > > > water molecules to the protein > > > , starting from a system of a solvated protein > > > ? > > > > > > Best, > > > Jose Borreguero > > > -- > > > 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. > > -- > > 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. -- 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] Remove all but N closest water molecules from protein
Hi Mark, Does your solution output variable numbers of water molecules per frame? That is exactly what I've been wanting to do for a while, but with my solution it becomes very difficult to do so and I usually end up using a fixed number of closest waters for all frames. João On Thu, Jun 8, 2017 at 10:34 AM, Mark Abraham wrote: > Hi, > > Or gmx select to make an index group for the nearest waters, and gmx > trjconv to make the subset with the index group. > > Mark > > On Thu, Jun 8, 2017 at 9:05 AM João Henriques < > joao.m.a.henriq...@gmail.com> > wrote: > > > Hi, > > > > trjorder can reorder the water molecules in each frame according to their > > distance to the protein. Then you either manually prune the gro file(s) > or > > use an index file to get rid of the extra stuff. I don't know of any > native > > tool that does all of this in one step but I may be outdated regarding > new > > stuff on gmx 2016. > > > > Cheers, > > João > > > > On Jun 8, 2017 2:49 AM, "Jose Borreguero" wrote: > > > > Dear Gromacs users, > > > > I'm a newbie with Gromacs. Is there a Gromacs native tool that will allow > > me to create a new *.gro file containing the protein and the N closest > > water molecules to the protein > > , starting from a system of a solvated protein > > ? > > > > Best, > > Jose Borreguero > > -- > > 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. > -- > 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] Remove all but N closest water molecules from protein
Hi, Or gmx select to make an index group for the nearest waters, and gmx trjconv to make the subset with the index group. Mark On Thu, Jun 8, 2017 at 9:05 AM João Henriques wrote: > Hi, > > trjorder can reorder the water molecules in each frame according to their > distance to the protein. Then you either manually prune the gro file(s) or > use an index file to get rid of the extra stuff. I don't know of any native > tool that does all of this in one step but I may be outdated regarding new > stuff on gmx 2016. > > Cheers, > João > > On Jun 8, 2017 2:49 AM, "Jose Borreguero" wrote: > > Dear Gromacs users, > > I'm a newbie with Gromacs. Is there a Gromacs native tool that will allow > me to create a new *.gro file containing the protein and the N closest > water molecules to the protein > , starting from a system of a solvated protein > ? > > Best, > Jose Borreguero > -- > 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. -- 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] Remove all but N closest water molecules from protein
Hi, trjorder can reorder the water molecules in each frame according to their distance to the protein. Then you either manually prune the gro file(s) or use an index file to get rid of the extra stuff. I don't know of any native tool that does all of this in one step but I may be outdated regarding new stuff on gmx 2016. Cheers, João On Jun 8, 2017 2:49 AM, "Jose Borreguero" wrote: Dear Gromacs users, I'm a newbie with Gromacs. Is there a Gromacs native tool that will allow me to create a new *.gro file containing the protein and the N closest water molecules to the protein , starting from a system of a solvated protein ? Best, Jose Borreguero -- 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.
[gmx-users] Remove all but N closest water molecules from protein
Dear Gromacs users, I'm a newbie with Gromacs. Is there a Gromacs native tool that will allow me to create a new *.gro file containing the protein and the N closest water molecules to the protein , starting from a system of a solvated protein ? Best, Jose Borreguero -- 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.