VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Sat Jun 15 2019 - 17:05:15 CDT

Hi Roshan,

The DCD file has a header. The number of frames are written to it.
So if the header says 25000 frames, and you can go only until 13499, is
there a chance that the DCD file is corrupted? Did something happen while
you were running the simulation? Is dyn3.dcd a result of combining multiple
dcd files.

A number of things can result in DCD files going bad.

There is no easy way, in my head that can fix this. If you appended the DCD
files -- go and append them again, if you get the same result - perhaps
better to keep them separate.

If this is a single file and not a result of appending multiple smaller
trajectories together - then you will have to actually go inside the DCD
and skip the frames that are bad. This is not a trivial thing but can be
done. To confirm if possible I searched the mailing lists and found an
answer for you here:

https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2008-2009/1037.html

Best,
/A

On Sat, Jun 15, 2019 at 5:29 PM Roshan Shrestha <roshanpra_at_gmail.com> wrote:

> Hi everyone,
> I am using catdcd to skip the number of frames of the
> trajectory of my system. While using it to find the number of frames with
> *catdcd -num dyn3.dcd*
> gives:
> Opened file 'dyn3.dcd' for reading.
> Read 25000 frames from file dyn3.dcd.
> Total frames: 25000
> CatDCD exited normally.
> using it to skip the number of frames with
>
> *catdcd -o output.dcd -stride 10 dyn3.dcd *
> gives:
> Opened file 'dyn3.dcd' for reading.
> dcdplugin) read_dcdstep: corruption or unrecognized file structure
> Read 13499 frames from file dyn3.dcd, wrote 1349.
> Total frames: 13499
> Frames written: 1349
> CatDCD exited normally.
> So, read_dcdstep is showing me the error which I don't know why it is
> showing so that I am getting only 1349 frames instead of 2500 frames. What
> can be the issue and how can I resolve it.
>
> Thanks
>
>
> --
> *Roshan Shrestha*
> M.Sc (Physics)
> Central Department of Physics, Tribhuvan University
> Kathmandu, Nepal
>
>
>
> 

-- 
Best,
/A