Re: [gmx-users] problem with calculating angles and dynamic selections
Dear Venkat and Teemu, Thank you, that clarified the subject. Best, g On 2014-07-04 06:57, Teemu Murtola wrote: No, this is not a bug, but a result of a conscious design. Internally, the selections are always evaluated as sets of atoms, which are (currently) handled as a sorted list of indices. So any basic selection operation always results in sorted atoms. If you want something else, you can use "permute", "merge" or "plus" (which is only necessary for those few tools that put significance to the order of atoms). In addition to simplifying the implementation, this is much clearer. Or what order would you expect the atoms to be if you provide a selection "name C A B", and your system has 10 A atoms, 5 B atoms and 3 C atoms? How about if the system has molecules with multiple residues (so that splitting by molecule or by residue results in different ordering)? Or if you combine two arbitrary unsorted expressions with "and" or "or"? On Jul 3, 2014 8:04 PM, "Venkat Reddy" wrote: Hi, I have tried gmx gangle -g1 angle option. Its sorting the atoms specified in the input. I think it might be a bug. gmx gangle -g1 vector -g2 vector is doing fine. -- 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] problem with calculating angles and dynamic selections
No, this is not a bug, but a result of a conscious design. Internally, the selections are always evaluated as sets of atoms, which are (currently) handled as a sorted list of indices. So any basic selection operation always results in sorted atoms. If you want something else, you can use "permute", "merge" or "plus" (which is only necessary for those few tools that put significance to the order of atoms). In addition to simplifying the implementation, this is much clearer. Or what order would you expect the atoms to be if you provide a selection "name C A B", and your system has 10 A atoms, 5 B atoms and 3 C atoms? How about if the system has molecules with multiple residues (so that splitting by molecule or by residue results in different ordering)? Or if you combine two arbitrary unsorted expressions with "and" or "or"? On Jul 3, 2014 8:04 PM, "Venkat Reddy" wrote: > Hi, > I have tried gmx gangle -g1 angle option. Its sorting the atoms specified > in the input. I think it might be a bug. gmx gangle -g1 vector -g2 vector > is doing fine. > > > On Thu, Jul 3, 2014 at 7:42 PM, gigo wrote: > > > Hi! > > I find it impossible to calculate (some) angles between atoms using > > dynamic selection in 'gmx gangle' command. The problem is, that the > dynamic > > selection mechanism persistently sorts numbers of atoms specified in the > > input. So, if I have atoms A, B and C with ascending indexes, I am not > able > > to calculate angle B-A-C - I only get value for A-B-C, no matter how I > > order them in the command line. Is there any way to do it without writing > > an index file (which I have to parse anyway, because the same mechanism > > sorts atoms in 'gmx select'...)? If not, I will submit a feature request > on > > redmine - something like -nosort option... > > Regards, > > > > Grzegorz Wieczorek > > -- > > 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. > > > > > > -- > With Best Wishes > Venkat Reddy Chirasani > PhD student > Laboratory of Computational Biophysics > Department of Biotechnology > IIT Madras > Chennai > INDIA-600036 > -- > 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] problem with calculating angles and dynamic selections
Hi, I have tried gmx gangle -g1 angle option. Its sorting the atoms specified in the input. I think it might be a bug. gmx gangle -g1 vector -g2 vector is doing fine. On Thu, Jul 3, 2014 at 7:42 PM, gigo wrote: > Hi! > I find it impossible to calculate (some) angles between atoms using > dynamic selection in 'gmx gangle' command. The problem is, that the dynamic > selection mechanism persistently sorts numbers of atoms specified in the > input. So, if I have atoms A, B and C with ascending indexes, I am not able > to calculate angle B-A-C - I only get value for A-B-C, no matter how I > order them in the command line. Is there any way to do it without writing > an index file (which I have to parse anyway, because the same mechanism > sorts atoms in 'gmx select'...)? If not, I will submit a feature request on > redmine - something like -nosort option... > Regards, > > Grzegorz Wieczorek > -- > 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. > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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] problem with calculating angles and dynamic selections
Hi, Have you tried gmx gangle -g1 vector -g2 vector -group1 resname RES and name A B -group2 resname RES and name A C I have valid results using the above command. In fact, I didn't find any problem with -g1 angle also. On Thu, Jul 3, 2014 at 7:42 PM, gigo wrote: > Hi! > I find it impossible to calculate (some) angles between atoms using > dynamic selection in 'gmx gangle' command. The problem is, that the dynamic > selection mechanism persistently sorts numbers of atoms specified in the > input. So, if I have atoms A, B and C with ascending indexes, I am not able > to calculate angle B-A-C - I only get value for A-B-C, no matter how I > order them in the command line. Is there any way to do it without writing > an index file (which I have to parse anyway, because the same mechanism > sorts atoms in 'gmx select'...)? If not, I will submit a feature request on > redmine - something like -nosort option... > Regards, > > Grzegorz Wieczorek > -- > 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. > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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] problem with calculating angles and dynamic selections
Hi! I find it impossible to calculate (some) angles between atoms using dynamic selection in 'gmx gangle' command. The problem is, that the dynamic selection mechanism persistently sorts numbers of atoms specified in the input. So, if I have atoms A, B and C with ascending indexes, I am not able to calculate angle B-A-C - I only get value for A-B-C, no matter how I order them in the command line. Is there any way to do it without writing an index file (which I have to parse anyway, because the same mechanism sorts atoms in 'gmx select'...)? If not, I will submit a feature request on redmine - something like -nosort option... Regards, Grzegorz Wieczorek -- 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.
