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

[Teemu Murtola]

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
>> --
>> 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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>