VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri May 30 2003 - 16:02:50 CDT

Ioana,
  You didn't mention which version of VMD you're running, but I'm
assuming from your note that you ran the 32-bit version since you
referred to your machine being 32-bit. An Octane /w R10000 CPU
should be able to run the 64-bit version of VMD, though you probably
don't have enough physical memory to load a 4GB trajectory on your box.
You might try installing the 64-bit version of VMD in a test directory
on your machine and see if it can load your trajectory or not.

I've personally run VMD on 64-bit Sun machines with 16GB of physical memory,
and a big SGI Onyx with 12GB, and I know that one can load HUGE trajecotories
on machines of this size, so you ought to be able to get this working
if you run the right VMD binary on a fairly capable 64-bit machine with
a decent amount of memory.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, May 30, 2003 at 01:56:08PM -0700, Ioana Cozmuta wrote:
> Hi John,
>
> Sorry for not giving enough detail. I have the dcd file on my local
> machine so I do not attempt to load it over the network. My local machine
> is a 32-bit machine, an SGI Octane dual (R10000), operating system Irix64
> version 6.5. Swap memory is 2Gb (so I've asked my sys admin to increase
> it, maybe it will help me solve the problem).
> I am using vmd_1.8.
> The file was generated on 64-bit SGI machine, R14k.
>
> I did not try it yet but I was thinking that it may be possible to use a
> logfile on the 64-bit machine and run vmd to generate a movie there and
> then only visualize it on my local machine although this allows me less
> flexibility in what frames I want to focus on.
>
> Any suggestion would be appreciated. Thanks,
> Ioana
>
>
> On Fri, 30 May 2003, John Stone wrote:
>
> >
> > 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
> > 

-- 
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