From: Axel Kohlmeyer (
Date: Mon Oct 08 2007 - 11:41:09 CDT

On Mon, 8 Oct 2007, weilin Zhang wrote:

WZ> Hi

dear weilin,

your problem report is missing two essential pieces of information:
1) the name and version of your operating system
2) the version of VMD

without that, we can only use 'the force' to figure out what is
happening and whether this is a new problem or something that
we already know about or whether this is not VMD's fault at all.

WZ> I have been in a strange situation that I could not find any solution
WZ> from previous mail list.
WZ> My vmd crashes when I attempted to load a .pdb file when I simply run vmd.
WZ> Either
WZ> vmd xxx.pdb
WZ> or load new molecule->xxx.pdb
WZ> will terminate the current vmd program.
WZ> However when I have psf and the crd file, it works.
WZ> Very strangely, according to some previous information I run a debug mode:
WZ> vmd -debug.
WZ> (gdb)run
WZ> then I load pdb file it works. Does it mean that there is no problem
WZ> with all those libraries thing?

no. but it looks a lot like you are running a redhat enterprise linux
version 4 or a clone of it, that has an old kernel with a bug in
the multi-threading support and you are using VMD version 1.8.6.
if that is the case, please check again the linux release notes
and update your operating system. the workaround would be to
enforce that VMD runs single threaded, but it don't know whether
it is a good idea to run with a kernel that has a bug in multi-thread
support. to explain the problem: in VMD 1.8.6 the bond search
code is multi-threaded. if you use a .psf file this code is
not used. in case of using the debugger, you should run
single threaded... or you just got lucky...


WZ> Thank you for your advice
WZ> Weilin

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.