[gmx-users] Analysis of old xtc file using gromacs-5 tools

[Venkat Reddy]

Hi Teemu,
Thank you for providing the patch. But the patched version is giving
following error message:

Program:     gmx rdf, VERSION 5.2-dev
Source file: src/gromacs/utility/path.cpp (line 406)
Function:    static void gmx::File::throwOnError(const
gmx::File::NotFoundInfo&)

System I/O error:
Failed to access file 'traj.xtc'.
The file could not be opened.
  Reason: Value too large for defined data type
  (call to fopen() returned error code 75)

I would like to inform you that I have installed this patched version to a
non-standard location.


On Wed, Sep 30, 2015 at 8:39 AM, Teemu Murtola <teemu.murtola at gmail.com>
wrote:

> Hi,
>
> I now changed the check to provide more details (in 5140
> <https://gerrit.gromacs.org/5140>). If you haven't figured out what the
> issue was, you could try building the source code from the above link, and
> running it to get more details.
>
> There is not much we can do to help diagnose the issue further, unless you
> can provide additional information on the file system contents. Also note
> that if you provide an input file name that looks like a valid file name
> (with the correct extension), Gromacs 5.1 will use it as is, or give an
> error if it does not exist. Previous versions silently tried to append all
> kinds of extensions if the file did not exist (or could not be read) even
> in such a case, and could then use some other file as input.
>
> Best regards,
> Teemu
>
> On Sat, Sep 26, 2015 at 11:56 AM Teemu Murtola <teemu.murtola at gmail.com>
> wrote:
>
> > This error has nothing to do with the contents of the file, but rather
> the
> > operating system appears to be telling Gromacs that the file cannot be
> > opened or that it is not a regular file. With the information here, it's
> > difficult to say anything more; if you want to debug this further, the
> > relevant function is gmx::File::exists().
> >
> > It would be useful to know what's the problem so that the check (or the
> > error message) can be improved.
> >
> > Best regards,
> > Teemu
> >
> > On Fri, Sep 25, 2015, 21:20 Venkat Reddy <venkat4bt at gmail.com> wrote:
> >
> >> Hi Tsjerk,
> >> Thank you for the quick reply. Yes I can access it with other versions,
> >> like 4.5.5, 5.0.4.
> >>
> >> On Fri, Sep 25, 2015 at 11:33 PM, Tsjerk Wassenaar <tsjerkw at gmail.com>
> >> wrote:
> >>
> >> > Hi Venkat,
> >> >
> >> > Does it exist? Is it accessible? The XTC format did not change since
> the
> >> > early years of Gromacs. Can you access it with a different version?
> >> >
> >> > Cheers,
> >> >
> >> > Tsjerk
> >> > On Sep 25, 2015 19:52, "Venkat Reddy" <venkat4bt at gmail.com> wrote:
> >> >
> >> > > Dear all,
> >> > > I have a trajectory file generated by gromacs-4.5.5. Recently I
> tried
> >> to
> >> > > plot radial distribution function using 'gmx rdf' tool available in
> >> > > gromacs-5.1. But I am getting the following error.
> >> > > Error in user input:
> >> > > Invalid command-line options
> >> > >   In command-line option -f
> >> > >     File 'system.xtc' does not exist or is not accessible.
> >> > >
> >> > > I knew that gromacs old trajectories can be analysed using new
> version
> >> > > tools. But why I am facing this error?
> >> > >
> >> > >
> >> > > With regards
> >> > > Venkat Reddy Chirasani
> >> > > PhD student
> >> > > Laboratory of Computational Biophysics
> >> > > Department of Biotechnology
> >> > > IIT Madras
> >> > > Chennai
> >> > > INDIA-600036
> >> > > --
> >> > > Gromacs Users mailing list
> >> > >
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> >> > > posting!
> >> > >
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> or
> >> > > send a mail to gmx-users-request at gromacs.org.
> >> > >
> >> > --
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> >> >
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> >> >
> >>
> >>
> >>
> >> --
> >> 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
> >>
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> >> send a mail to gmx-users-request at gromacs.org.
> >>
> >
> --
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>
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>



-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036