[gmx-users] Viewing gromacs .xtc trajectory 'Error reading timestep, file does not match format'

[Mark Abraham]

OK, that suggests the file itself is fine. 5000fs per frame times 4000
frames is suspiciously close to 2^31... might there be a 32-bit limitation
going on here? Otherwise, use trjconv to chop up your trajectory and get
access to it that way.

Mark

On Thu, Jun 25, 2015 at 5:01 PM Vidyalakshmi CM <vidyalakshmi.cm at gmail.com>
wrote:

> Dear Sir,
>
> I used the gromacs gmxcheck command and I got the following output display:
>
> Item        #frames Timestep (ps)
> Step          4840    5
> Time          4840    5
> Lambda           0
> Coords        4840    5
> Velocities       0
> Forces           0
> Box           4840    5
>
> Therefore the total number of frames in the file seems to be correct and
> also read by the gromacs program.
>
> In such cases what could be the possible reason.
>
> Thanks and Best Regards,
> C.M.Vidyalakshmi
>
>
>
>
>
>
> On Thu, Jun 25, 2015 at 3:23 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > You can use gmxcheck / gmx check to examine the file and perhaps get some
> > more information, but this sounds like something has mis-managed your
> file.
> > e.g. you didn't construct it how you think you did, or the (parallel)
> file
> > system upon which you ran mdrun is not reliable.
> >
> > Mark
> >
> > On Thu, Jun 25, 2015 at 3:34 PM Vidyalakshmi CM <
> vidyalakshmi.cm at gmail.com
> > >
> > wrote:
> >
> > > Dear All,
> > >
> > > I am trying to visualize the gromacs output .xtc trajectory on VMD. I
> am
> > > generating .xtc trajectory frames every 5 ps. The total simulation run
> > time
> > > is 24195 ps which should give me 4839 frames (without any skip).
> However,
> > > when I load frames say 4000 to 4100, I get the error message 'Error
> > reading
> > > timestep, file does not match format'.
> > >
> > > With a skip of 10, I find the trajectory loads only initial frames
> (~200
> > > frames out of more than 480 which is expected).
> > >
> > > I have used VMD for viewing .xtc trajectories previously and have never
> > had
> > > this issue previously.
> > >
> > > Please help.
> > >
> > > Thanks and Best Regards,
> > > C.M.Vidyalakshmi
> > > --
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