VMD-L Mailing List

From: Nichols A. Romero (naromero_at_gmail.com)
Date: Sat Mar 31 2007 - 18:11:30 CDT

I figured out what the problem was and found a simple work around so
the problem I encountered would not occur in the future.

Thanks for your dedications to the users on this list.

On 3/29/07, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> Are the CP2K DCDs being corrupted only under certain conditions
> (e.g. if the program terminates abnormally) or is this a consistent
> problem? You could write a Tcl script in VMD to reconstruct the
> damaged DCD header if you knew what attributes it had before it
> got corrupted, e.g. the atom count, whether there were fixed atoms,
> which DCD format variant it was, file endianism, etc.
>
> Most likely the time-economical solution would be to work with the CP2K
> authors and figure out why the header is getting corrupted, and help them
> get their DCD writing code fixed. The CP2K authors might want to look
> at NAMD to see how it writes its DCD files. NAMD tries very hard to
> deal with supercomputers that have flaky I/O subsystems, and recover
> gracefully from various error situations as best it can.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, Mar 29, 2007 at 11:21:31AM -0400, Nichols A. Romero wrote:
> > Hi,
> >
> > I saw similar topics discussed on this forum but mine may be slightly
> > different.
> >
> > I am doing ab initio MD using CP2K.
> > http://cp2k.berlios.de/
> >
> > Occasionally, it seems like the DCD files that are created don't write
> the
> > header
> > information (or part of it). This seems related to restarts, but I am
> not
> > 100% sure,
> > but this occasionally does happen.
> >
> > In any case, given this 'damaged' DCD file is there anyway to figure out
> > what part of the
> > header is missing and then add the missing information.
> >
> > I have that matdcd m-files tools if that helps.
> >
> > P.S. I do not believe this is related to a different DCD version, as I
> have
> > been able to
> > read DCD files which are compliant with the most recent DCD standard.
> >
> >
> >
> > --
> > Nichols A. Romero, Ph.D.
> > 1613 Denise Dr. Apt. D
> > Forest Hill, MD 21050
> > 443-567-8328 (C)
> > 410-306-0709 (O)
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> 

-- 
Nichols A. Romero, Ph.D.
1613 Denise Dr. Apt. D
Forest Hill, MD 21050
443-567-8328 (C)
410-306-0709 (O)