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 <[email protected]> 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 <[email protected]> > 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 <[email protected]> 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 <[email protected]> > >> 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" <[email protected]> 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 [email protected]. > >> > > > >> > -- > >> > 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 [email protected]. > >> > > >> > >> > >> > >> -- > >> 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 [email protected]. > >> > > > -- > 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 [email protected]. > -- 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 [email protected].
