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

[Vidyalakshmi CM]

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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