VMD-L Mailing List

From: Vidyalakshmi CM (vidyalakshmi.cm_at_gmail.com)
Date: Thu Jun 25 2015 - 10:39:21 CDT

Dear Sir,

The gromacs analysis/check programs were performed on the same computer
platform (like linux).

The version of VMD I am using is VMD 1.9.1.

Is there a way to check if VMD is reading the file correctly.

Thanks and Best Regards,
C.M.Vidyalakshmi

On Thu, Jun 25, 2015 at 4:29 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Thu, Jun 25, 2015 at 10:37 AM, Vidyalakshmi CM
> <vidyalakshmi.cm_at_gmail.com> wrote:
> > 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)
>
> did you run those gromacs analysis/check programs on windows?
> otherwise it is not a convincing argument.
>
> which version of VMD are you using?
>
> > So, it looks like the number of files in the output trajectory are
> correct
> > but they are not appearing in VMD.
>
> unless you can provide me with a convincing proof that VMD is failing
> on correct files, there is little that can be done.
>
> axel.
>
> > 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.
> >
> >
>
>
>
> --
> 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.
>