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

Thu Oct 1 08:01:54 CEST 2015

Hi
Gromacs-5.1 version can not read xtc files. However, it can access single
frame gro/pdb files.

On Thu, Oct 1, 2015 at 10:44 AM, Teemu Murtola <teemu.murtola at gmail.com>
wrote:

> Are you saying that you cannot open any xtc files? If that is the case,
> then this may not have anything to do with 64-bit for support. Can your
> Gromacs compilation open any files? You will need to isolate the problem a
> bit to help diagnosing it, since we don't have access to your system.
>
> Teemu
>
> On Thu, Oct 1, 2015, 07:48 Venkat Reddy <venkat4bt at gmail.com> wrote:
>
> > Hi,
> > 1) Yes, I can access the same xtc with older gromacs versions.
> > 2) I can't access even smaller xtc files with 5.1
> > I will file a bug report for the same.
> > Thank you
> >
> >
> >
> > On Wed, Sep 30, 2015 at 9:28 PM, Teemu Murtola <teemu.murtola at gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > This sounds like the build system is not compiling Gromacs with 64-bit
> > file
> > > support like it should. Can you access the same file on the same system
> > > with earlier Gromacs versions? Can you access smaller files with 5.1?
> > >
> > > Could you file a bug report at redmine.gromacs.org, and include at
> least
> > > the following:
> > > * information on your operating system
> > > * contents of CMakeCache.txt, src/config.h, and src/gmxpre-config.h
> from
> > > your build tree
> > > * how you invoked cmake to configure the build.
> > >
> > > Teemu
> > >
> > > On Wed, Sep 30, 2015, 11:59 Venkat Reddy <venkat4bt at gmail.com> wrote:
> > >
> > > > 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
> > > > > > > >> > > --
> > > > > > > >> > > Gromacs Users mailing list
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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
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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
> > > > > > --
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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