VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri May 30 2003 - 10:29:32 CDT

Ioana,
  You didn't mention what platform you're using? Since this
trajectory file is quite large, it is possible that you have run
into problems with 32-bit file offsets, 32-bit NFS, or that you
ran out of physical memory on the machine you're attempting to load
the trajectory on with VMD. How much physical memory does your machine
have? Tell me which version of VMD you're using, and whether
this file is local to the machine, or accessed over the network
via NFS or Samba and I may have some suggestions for you. The error you're
getting looks suspiciously like a 32-bit filesystem problem of one type
or another. People in our lab commonly work with trajectory files much
larger than 4GB, but we're using 64-bit file servers that correctly deal
with large files, and we use both 64-bit Sun workstations,
and various Linux machines that have recent kernels, both of which
deal with large files correctly.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, May 29, 2003 at 05:53:40PM -0700, Ioana Cozmuta wrote:
> Hi vmd-users,
>
> I did run NPT dynamics (it is a continuation of a previous run) and I
> want to load the dcd trajectory in vmd.
> I load first the initial pdb file (on which I've started the dynamics) and
> then on top of that I select to load the dcd trajectory. However I get the
> following message and there is no frame loaded
>
> Info) Finished with coordinate file
> /stor2/ioana/chapman_runs/pore_1K/diffK/Kdiff.dcd
>
> The file exists and has quite a big size:
> -rw------- 1 ioana rtc 3919404696 May 29 16:01 Kdiff.dcd
>
> it is supposed to have 4000 frames.
>
> Did this happen to anyone else? Does anyone have any idea what could be
> wrong?
>
> Thanks a lot,
> Ioana 

-- 
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