[gmx-users] How to make a program run on the trajectory

[João Henriques]

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 <prasun30 at gmail.com> 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 <dgilgmx at gmail.com> 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.32353 at 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 <prasun30 at gmail.com
> > > <javascript:;>> 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-request at gromacs.org <javascript:;>.
> > > >
> > > --
> > > 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-request at gromacs.org <javascript:;>.
> > --
> > 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-request at 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-request at gromacs.org.
>