From: Axel Kohlmeyer (
Date: Mon Oct 08 2007 - 12:10:07 CDT

On Mon, 8 Oct 2007, weilin Zhang wrote:

WZ> Hi Axel

dear weilin,
WZ> Thanks to your advice and suggestion for tips of post.
WZ> I will post such version information in my future post.
WZ> My system is Just Redhat enterprise Linux 4!
WZ> Have this been showed on mail-list?

yes. we had a couple of cases that had the same problem.

WZ> How could I do so?

how to update the OS is not the topic of the VMD list.
if you have a subscription with red hat, please follow
the instructions given by red hat. if not, i suggest
you update to CentOS 4.5, which is essentially red hat
EL 4.5 and would give you a binary compatible and up-to-date


WZ> Many thanks and best wishes
WZ> Weilin
WZ> Axel Kohlmeyer wrote:
WZ> > On Mon, 8 Oct 2007, weilin Zhang wrote:
WZ> >
WZ> > WZ> Hi
WZ> >
WZ> > dear weilin,
WZ> >
WZ> > your problem report is missing two essential pieces of information:
WZ> > 1) the name and version of your operating system
WZ> > 2) the version of VMD
WZ> >
WZ> > without that, we can only use 'the force' to figure out what is
WZ> > happening and whether this is a new problem or something that
WZ> > we already know about or whether this is not VMD's fault at all.
WZ> >
WZ> > WZ> I have been in a strange situation that I could not find any solution
WZ> > WZ> from previous mail list.
WZ> > WZ> My vmd crashes when I attempted to load a .pdb file when I simply run vmd.
WZ> > WZ> Either
WZ> > WZ> vmd xxx.pdb
WZ> > WZ> or load new molecule->xxx.pdb
WZ> > WZ> will terminate the current vmd program.
WZ> > WZ>
WZ> > WZ> However when I have psf and the crd file, it works.
WZ> > WZ> Very strangely, according to some previous information I run a debug mode:
WZ> > WZ> vmd -debug.
WZ> > WZ>
WZ> > WZ> (gdb)run
WZ> > WZ> then I load pdb file it works. Does it mean that there is no problem
WZ> > WZ> with all those libraries thing?
WZ> >
WZ> > no. but it looks a lot like you are running a redhat enterprise linux
WZ> > version 4 or a clone of it, that has an old kernel with a bug in
WZ> > the multi-threading support and you are using VMD version 1.8.6.
WZ> > if that is the case, please check again the linux release notes
WZ> > and update your operating system. the workaround would be to
WZ> > enforce that VMD runs single threaded, but it don't know whether
WZ> > it is a good idea to run with a kernel that has a bug in multi-thread
WZ> > support. to explain the problem: in VMD 1.8.6 the bond search
WZ> > code is multi-threaded. if you use a .psf file this code is
WZ> > not used. in case of using the debugger, you should run
WZ> > single threaded... or you just got lucky...
WZ> >
WZ> > cheers,
WZ> > axel.
WZ> >
WZ> > WZ>
WZ> > WZ> Thank you for your advice
WZ> > WZ>
WZ> > WZ> Weilin
WZ> > WZ>
WZ> >
WZ> >

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.