VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun May 23 2004 - 15:40:35 CDT

Hi Esben,
  Ilja sent me a copy of Charmm PSF/CRD files generated on itanium, we'll
have a look and determine if this is just an endianness problem or an actual
word size issue. If the latest version of our Charmm coordinate file reader
doesn't load it, then we'll have to see if we can make changes to it so it
does. With any luck we'll have a solution for this soon.

  John Stone
  vmd_at_ks.uiuc.edu

On Sun, May 23, 2004 at 10:31:55PM +0200, EPF (Esben Peter Friis) wrote:
>
> Hi Ilja and VMD'ers :-)
>
> (Typo? You refer to .crd files as trajectories - Charmm trajectories are normally called .dcd . It may be possible to store the trajectory as a .crd file, but they are text files, and should have no problems when transferred between architectures.)
>
> I have no experience with Itanium or Itanium2, but CHARMM (or NAMD)trajectories (.dcd) created on a SGI Octane (64bit MIPS R10000) can be read directly by VMD on a 32bit machine. I would expect that only the endianism (byte order) is different in the files.
>
>
> Cheers,
>
> Esben
>
>
> -----Original Message-----
> From: owner-vmd-l_at_ks.uiuc.edu
> To: ILJA Khavrutskii
> Cc: vmd-l_at_ks.uiuc.edu
> Sent: 23-05-04 02:45
> Subject: Re: vmd-l: How to read i8(64 bit) .crd file with 32 bit VMD
>
>
> Hi,
> I don't have any 64-bit Charmm CRD files to test with, so at present
> its unlikely that _any_ version of VMD would read them if they differ
> substantially from normal ones. If you can provide us with examples
> of such files, we could try make them work on 32-bit machines.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Sat, May 22, 2004 at 10:07:23AM -0700, ILJA Khavrutskii wrote:
> > Dear VMD people,
> >
> > Can vmd built for 32 bit linux machine (such as Xeon) read CHARMM
> > trajectory (*.crd) generated on 64 bit machine (such as Itanium2)?
> > I know the work around it via DYNA FORM/DYNA UNFO to transfer files
> > between architectures, but was hoping that there might be an easy way
> in
> > VMD.
> >
> > Has anyone compiled VMD on Itanium2 machines, to be able to view i8
> > CHARMM trajectories?
> >
> > Sincerely,
> > Ilja
> >
>
> --
> 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