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

Wed Sep 30 08:01:46 CEST 2015

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
> > >> > >
> > >> > > * 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.
> > >> >
> > >>
> > >>
> > >>
> > >> --
> > >> 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
> > >>
> > >> * 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.
> >
>
>
>
> --
> 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
>
> * 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.
>