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

Wed Sep 30 10:59:14 CEST 2015

Hi Teemu,
Thanks for the prompt reply. Yes, the xtc file size is larger than 2GB
(approx. 50GB) and both system.xtc and traj.xtc are same files. I am
extremely sorry for the confusion :)

On Wed, Sep 30, 2015 at 11:31 AM, Teemu Murtola <teemu.murtola at gmail.com>
wrote:

> Thanks for testing it, I see that there is still room for improvement in
> getting more context information into the error messages. I'm a bit
> confused by the difference between your original report of system.xtc vs
> traj.xtc in the new message, but that may not matter that much. Is your xtc
> file larger that 2GB in size?
>
> On Wed, Sep 30, 2015, 07:53 Venkat Reddy <venkat4bt at gmail.com> wrote:
>
> > 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
> > > >> > > --
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> > > >> --
> > > >> With Best Wishes
> > > >> Venkat Reddy Chirasani
> > > >> PhD student
> > > >> Laboratory of Computational Biophysics
> > > >> Department of Biotechnology
> > > >> IIT Madras
> > > >> Chennai
> > > >> INDIA-600036
> > > >> --
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> >
> > --
> > With Best Wishes
> > Venkat Reddy Chirasani
> > PhD student
> > Laboratory of Computational Biophysics
> > Department of Biotechnology
> > IIT Madras
> > Chennai
> > INDIA-600036
> > --
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-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036