VMD-L Mailing List

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Fri May 30 2003 - 19:15:14 CDT

Hi John,

Thanks for your advice, I've downloaded the 64bit version and it works
(with the increased swap space available now on my machine).

Ioana

On Fri, 30 May 2003, John Stone wrote:

>
> 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
>