From: Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Tue Jan 10 2006 - 10:59:14 CST
Regarding the first question, you shouldn't have any problem at loading dcd files in either 32 or 64-bit machines. For example, I usually run my simulations using an Altix cluster (64 bits) and perform the analysis in a PC running under Linux or Windows (32 bits). I don't know exactly what's your problem, but I've been using catDCD to cut very big dcd files and I haven't encounter any problem.
Second, what do you mean with "recover" a part of the trajectory?
From: owner-namd-l_at_ks.uiuc.edu on behalf of Jorge Pikunic
Sent: Tue 1/10/2006 10:20 AM
Subject: RE: namd-l: problems reading large dcd file
Thank you and others for replying. It seems that the version of NAMD that I
was using was compiled in 32 bit. The dcd files are 2.2GB. I have the
following questions (maybe the developers can help answering these):
1. Is it likely that the dcd files have been corrupted due to the 32 bit
2. Is there any way of recovering at least part of the trajectory stored in
those dcd files?
Dr. Jorge Pikunic
Department of Biochemistry
University of Oxford
South Parks Road
Oxford OX1 3QU
> -----Original Message-----
> From: Joshua D. Moore [mailto:jdmoore_at_unity.ncsu.edu]
> Sent: 07 January 2006 5:23 AM
> To: jorge.pikunic_at_bioch.ox.ac.uk
> Cc: namd-l_at_ks.uiuc.edu
> Subject: Re: namd-l: problems reading large dcd file
> 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
> Email: jdmoore_at_unity.ncsu.edu
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