Re: [gmx-users] How to make a program run on the trajectory
Ok, I think I follow you now. The simplest and easiest (not the most elegant and fast tough) answer is: do more or less what do_dssp/DSSP do together. Just print a PDB per each consecutive frame (using "trjconv") and run your program on each one. You now either save one output per PDB and do the statistics at the end, or you just keep all the information in virtual memory and output the final results at the end. Depends on what takes the least modification to your existing code. *IMPORTANT NOTE:* As you probably know better than me, having stuff stored in virtual memory is way faster than read/write from/to the disk. In the ideal world, you really want to avoid that. *The best/most efficient solution would be to load the binary trajectory (e.g. xtc file) into memory and operate directly on that information.* However, that will probably involve a lot of coding, and thus it all comes down to what takes less time: Writing a high performance program from scratch? Or running a less elegant solution that uses the code you already have? Hope it helps! Cheers, João On Tue, Sep 20, 2016 at 7:49 AM, prasun kumar wrote: > Dear João and Dan > > Thank you for the response and I am sorry for the confusion. > > I will try explaining my query with one example: > > In GROMACS, there are many programs available for the analyses of the > trajectory. One of them is "do_dssp". > For this purpose, one need to have dssp installed locally. > > Similarly, I have written a program that runs on a PDB or gro file. Now I > want to make it run on a trajectory and seek guidance. > > Hope I have made my point clear. > > > Regards > PK > > PRASUN (ASHOKA) > Desire + stability = Resolution > Resolution + Hard work = Success > > On Mon, Sep 19, 2016 at 3:43 AM, Dan Gil wrote: > > > Hi Prasun, > > > > Does your question have to do with reading the .trr format? > > > > If you want, you could convert it into a friendlier format such as .gro. > > Use gromacs trjconv to convert from .trr to .gro format. > > > > Best Regards, > > > > Dan > > > > On Saturday, September 17, 2016, João Henriques < > > joao.henriques.32...@gmail.com> wrote: > > > > > Dear Prasun, > > > > > > I am genuinely puzzled by your email. If taken literally, I'd have to > > > assume that you are stating that you don't know how to feed the > > trajectory > > > file as an argument to your programs, but that doesn't make any sense, > > > given that you explicitly say that you coded the programs yourself. If > > you > > > can code tools to run over binary files, such trivial matter can't be > the > > > problem here... > > > > > > Therefore, could you please state more specifically what is it that you > > > can't accomplish? Please be more verbose as well, it should help. > > > > > > Thank you, > > > João > > > > > > On Fri, Sep 16, 2016 at 8:23 PM, prasun kumar > > > wrote: > > > > > > > Hello > > > > > > > > I have written some programs in Fortran and PERL. > > > > Now I want to make them run on a trajectory file (.trr). > > > > Can some body guide me for the same. I believe that it must be > > available > > > on > > > > net. However, I was not able to find so. > > > > > > > > Thanx in advance. > > > > > > > > Regards > > > > Prasun > > > > > > > > PRASUN (ASHOKA) > > > > Desire + stability = Resolution > > > > Resolution + Hard work = Success > > > > -- > > > > 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. > -- Gromac
Re: [gmx-users] How to make a program run on the trajectory
Dear João and Dan Thank you for the response and I am sorry for the confusion. I will try explaining my query with one example: In GROMACS, there are many programs available for the analyses of the trajectory. One of them is "do_dssp". For this purpose, one need to have dssp installed locally. Similarly, I have written a program that runs on a PDB or gro file. Now I want to make it run on a trajectory and seek guidance. Hope I have made my point clear. Regards PK PRASUN (ASHOKA) Desire + stability = Resolution Resolution + Hard work = Success On Mon, Sep 19, 2016 at 3:43 AM, Dan Gil wrote: > Hi Prasun, > > Does your question have to do with reading the .trr format? > > If you want, you could convert it into a friendlier format such as .gro. > Use gromacs trjconv to convert from .trr to .gro format. > > Best Regards, > > Dan > > On Saturday, September 17, 2016, João Henriques < > joao.henriques.32...@gmail.com> wrote: > > > Dear Prasun, > > > > I am genuinely puzzled by your email. If taken literally, I'd have to > > assume that you are stating that you don't know how to feed the > trajectory > > file as an argument to your programs, but that doesn't make any sense, > > given that you explicitly say that you coded the programs yourself. If > you > > can code tools to run over binary files, such trivial matter can't be the > > problem here... > > > > Therefore, could you please state more specifically what is it that you > > can't accomplish? Please be more verbose as well, it should help. > > > > Thank you, > > João > > > > On Fri, Sep 16, 2016 at 8:23 PM, prasun kumar > > wrote: > > > > > Hello > > > > > > I have written some programs in Fortran and PERL. > > > Now I want to make them run on a trajectory file (.trr). > > > Can some body guide me for the same. I believe that it must be > available > > on > > > net. However, I was not able to find so. > > > > > > Thanx in advance. > > > > > > Regards > > > Prasun > > > > > > PRASUN (ASHOKA) > > > Desire + stability = Resolution > > > Resolution + Hard work = Success > > > -- > > > 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] How to make a program run on the trajectory
Hi Prasun, Does your question have to do with reading the .trr format? If you want, you could convert it into a friendlier format such as .gro. Use gromacs trjconv to convert from .trr to .gro format. Best Regards, Dan On Saturday, September 17, 2016, João Henriques < joao.henriques.32...@gmail.com> wrote: > Dear Prasun, > > I am genuinely puzzled by your email. If taken literally, I'd have to > assume that you are stating that you don't know how to feed the trajectory > file as an argument to your programs, but that doesn't make any sense, > given that you explicitly say that you coded the programs yourself. If you > can code tools to run over binary files, such trivial matter can't be the > problem here... > > Therefore, could you please state more specifically what is it that you > can't accomplish? Please be more verbose as well, it should help. > > Thank you, > João > > On Fri, Sep 16, 2016 at 8:23 PM, prasun kumar > wrote: > > > Hello > > > > I have written some programs in Fortran and PERL. > > Now I want to make them run on a trajectory file (.trr). > > Can some body guide me for the same. I believe that it must be available > on > > net. However, I was not able to find so. > > > > Thanx in advance. > > > > Regards > > Prasun > > > > PRASUN (ASHOKA) > > Desire + stability = Resolution > > Resolution + Hard work = Success > > -- > > 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] How to make a program run on the trajectory
Dear Prasun, I am genuinely puzzled by your email. If taken literally, I'd have to assume that you are stating that you don't know how to feed the trajectory file as an argument to your programs, but that doesn't make any sense, given that you explicitly say that you coded the programs yourself. If you can code tools to run over binary files, such trivial matter can't be the problem here... Therefore, could you please state more specifically what is it that you can't accomplish? Please be more verbose as well, it should help. Thank you, João On Fri, Sep 16, 2016 at 8:23 PM, prasun kumar wrote: > Hello > > I have written some programs in Fortran and PERL. > Now I want to make them run on a trajectory file (.trr). > Can some body guide me for the same. I believe that it must be available on > net. However, I was not able to find so. > > Thanx in advance. > > Regards > Prasun > > PRASUN (ASHOKA) > Desire + stability = Resolution > Resolution + Hard work = Success > -- > 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] How to make a program run on the trajectory
Hello I have written some programs in Fortran and PERL. Now I want to make them run on a trajectory file (.trr). Can some body guide me for the same. I believe that it must be available on net. However, I was not able to find so. Thanx in advance. Regards Prasun PRASUN (ASHOKA) Desire + stability = Resolution Resolution + Hard work = Success -- 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.