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

[prasun kumar]

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!
> >
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> >
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> > send a mail to gmx-users-requ...@gromacs.org .
> --
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>
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Re: [gmx-users] How to make a program run on the trajectory

[Dan Gil]

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

[João Henriques]

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

[prasun kumar]

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!

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