VMD-L Mailing List

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Sat Aug 20 2005 - 11:22:16 CDT

This is indeed the case. I tried writing out files at stride 10 and didn't
get what I expected; 77 files instead of 250. So catdcd is more
permissive than vmd
 On Fri, 19 Aug 2005, Justin Gullingsrud wrote:

> catdcd 2.x was extremely permissive: it counted frames by looking at
> just the dcd header. catdcd3.x, when counting frames, is basically
> just checking that the file size is correct; it doesn't actually read
> any data. What happens when you use catdcd and actually write to an
> output file?
>
> Justin
>
> On 8/19/05, Brian Bennion <brian_at_youkai.llnl.gov> wrote:
> >
> >
> > Hi John and others,
> >
> > I have a 3.1GB file generated by namd on a linux cluster Xeon cpus.
> > Catdcd reads through it and returns the proper number of frames.
> >
> > catdcd -num file.dcd
> > gives 2500 frames
> >
> >
> > However, I tried to load it into vmd and it files before the first frame
> > with error -4.
> >
> > Looking at the source code for readdcd.h -4 means a bad read
> > Diving deeper it seems it could fail with this error at a large number of
> > points during a dcd read so I don't know where the error is actually
> > caught.
> >
> > Is catdcd more tolerant of larger/corupted files than the vmd plugins?
> >
> > Brian
> >
> >
> > ************************************************
> > Brian Bennion, Ph.D.
> > Bioscience Directorate
> > Lawrence Livermore National Laboratory
> > P.O. Box 808, L-448 bennion1_at_llnl.gov
> > 7000 East Avenue phone: (925) 422-5722
> > Livermore, CA 94550 fax: (925) 424-6605
> > ************************************************
> >
> >
>
>
> --
> The spirit of Plato dies hard. We have been unable to escape the
> philosophical tradition that what we can see and measure in the world
> is merely the superficial and imperfect representation of an
> underlying reality.
> -- S.J. Gould, "The Mismeasure of Man"
>

************************************************
  Brian Bennion, Ph.D.
  Bioscience Directorate
  Lawrence Livermore National Laboratory
  P.O. Box 808, L-448 bennion1_at_llnl.gov
  7000 East Avenue phone: (925) 422-5722
  Livermore, CA 94550 fax: (925) 424-6605
************************************************