AMBER Archive (2006)

Subject: Re: AMBER: problem with amber 9 and igb=5

From: M. Scott Shell (
Date: Thu Jun 08 2006 - 10:55:36 CDT

John Mongan wrote:
> Can you be more specific about "hangs"? Does the program exit or stay
> running? Do you continue to see output to the mdout file? If you run
> top, is it using the maximum processor that it can, or is it
> stopped/blocked?
The program doesn't exit. The minout file is one byte in length and the
minimization program just continues to run. Right now I can't see the
process load because we're running it in a shared cluster without
individual node access.
> Also, what compiler and platform are you using?
We use "./configure g95" for Xeons running Linux version
2.6.16-1.2122_FC5smp ( (gcc
version 4.1.0 20060304 (Red Hat 4.1.0-3)) #1 SMP Sun May 21 15:18:32 EDT
> This seems very curious because igb=7 uses all of the code used by
> igb=5 (plus a little more for the neck correction).
After running many additional tests, I've found that the problem is not
specific to igb=5. It seems to occur regardless of the igb setting,
although it does not reproducibly occur every time sander is run. I've
also tried varying the PB radii set, and this doesn't seem to have an
effect either. This seems very unusual behavior to me; I'm wondering if
this could be some problem during compilation. Or could it be specific
to the pdb file which is used as an initial configuration, as I've only
seen this error when we use a pdb template in tleap? The pdb file we're
using seems quite reasonable.


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