VMD-L Mailing List

From: Vidyalakshmi CM (vidyalakshmi.cm_at_gmail.com)
Date: Thu Jun 25 2015 - 09:37:36 CDT

Dear Sir,

I am using gromacs module 4.6.5 on a computing platform for parallel
programming. I am working on this platform for the first time. And I am
finding the same problem in more than one trajectory output files obtained
from this system.

I tried to download the file to my local machine (using Winscp) once at
around 10 ns simulation (~2000 frames) and then I deleted this file in the
local machine and downloaded again after completion of the simulation.
(Such transfer of files on other computing platforms never resulted in
files getting corrupted).

The total number of entries in the log file is correct. And also when I am
using gromacs programs that read .xtc trajectory (like for rmsd
calculation), the number of timesteps read are correct ( i.e complete 24195
ps).

So, it looks like the number of files in the output trajectory are correct
but they are not appearing in VMD.

Please advise.

Thanks and Best Regards,
C.M.Vidyalakshmi

On Thu, Jun 25, 2015 at 2:56 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Thu, Jun 25, 2015 at 9:29 AM, 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). Please advise.
>
> this sounds like your trajectory file has been corrupted somehow.
>
> axel.
>
> >
> > 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
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>