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

Venkat Reddy venkat4bt at gmail.com
Mon Oct 5 07:31:38 CEST 2015

Sorry for the delay in reply.
I am able to access pdb/gro files of size 1.5 GB with Gromacs-5.1 version.
My Desktop is 32-bit whereas my xtc files were generated on our super
cluster, which runs on 64-bit O.S.

On Fri, Oct 2, 2015 at 9:46 AM, Teemu Murtola <teemu.murtola at gmail.com>

> Hi,
> On Thu, Oct 1, 2015 at 6:30 PM Szilárd Páll <pall.szilard at gmail.com>
> wrote:
> > On Thu, Oct 1, 2015 at 8:01 AM, Venkat Reddy <venkat4bt at gmail.com>
> wrote:
> > > Gromacs-5.1 version can not read xtc files. However, it can access
> single
> > > frame gro/pdb files.
> > >
> >
> > That's a bold claim that IMO requires equally strong proof.
> >
> I agree with Szilard. Are you saying that you cannot even read a
> single-frame xtc file with just a few kB in size? How about other binary
> files (e.g., trr)? How about large (>2GB) gro files?
> In your other mail to the list you were talking about a 32-bit Ubuntu VM.
> > Are you sure you're not running into in incompatibility issue between the
> > 32-bit binaries vs 64-bit xtc file(s) you're trying to read?
> >
> I would still suspect that the underlying reason is that for some reason,
> 5.1 gets compiled without large file support in your system, which makes
> even plain fopen() fail on large files. The build system should give an
> error if it cannot find 64-bit file support, but the check may be
> imperfect. Someone who can reproduce the issue (i.e., has access to a
> similar OS and other environment) should try what is actually required to
> get 64-bit file support working there. Based on the information you posted
> in Redmine, the build system already checks that off_t is 64-bit without
> any extra defines on your system. The checks in the build system have not
> changed between 5.0 and 5.1, though.
> Teemu
> --
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With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras

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