Re: problems reading large dcd file

From: Joshua D. Moore (
Date: Fri Jan 06 2006 - 23:22:43 CST

Hey Jorge,

I am not sure if you are having the same problem as me. You say different
system, do you mean different computer system? Anyway, my problem was
that the files were reaching their limit when I was running in 32 bit mode
on DataStar. This made the file size limit 2 GB, and the DCD files were
unreadable (by VMD and catdcd). I am now recompiling NAMD in 64 bit mode
and the people at SDSC say my problem should go away as there is no file
size limit.

I was having a similar problem with catdcd 4.0, but I think that my binary
may have been compiled in 32 bit. I used an old version of catdcd 3.0
before and I could combine files into larger than 2 GB so maybe it was 64
bit (not really sure).

Let me know if this is your problem or you find a solution.


On Fri, January 6, 2006 11:45 am, Jorge Pikunic wrote:
> Hello,
> I am having problems reading dcd files from simulations of a fairly
> large system (200,000 atoms). The size of each file is about 2.1 GB. I
> have tried doing:
> 1. catdcd: catdcd -num production_1.dcd , and I get:
> CatDCD 3.0
> read_dcdreader returned -6
> Error: could not open file 'production_1.dcd' for reading.
> 2. vmd: When I try to load the dcd file, after loading the psf file, I
> get "unable to load molecule". I get the same result even if I try to
> load only one frame.
> I have been able to read larger files from different systems (> 5 GB)
> with catdcd. Also, I can read smaller dcd files (1.7 GB) from shorter
> simulations of the same system. I have checked the NAMD output files,
> but there is nothing strange; NAMD wrote to dcd files periodically and
> there are no errors reported.
> Any ideas of what might be wrong?
> Thank you,
> Jorge

Joshua D. Moore
Graduate Student
North Carolina State University
Department of Chemical and Biomolecular Engineering
Box 7905 Centennial Campus
Engineering Building I
911 Partners Way
Raleigh, NC 27695-7905
Phone: (919) 513-2051
Fax: (919) 513-2470

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