RE: AMBER: sander crashes during minimization

From: Ross Walker <>
Date: Wed, 10 Jan 2007 11:40:05 -0800

Hi Seth,

We need more information to be able to help here. What is written to the
output file. What does your mdin file look like. Can we see the prmtop and
inpcrd files. How many atoms, what type of simulation, how many steps before
the segfault? Any other error messages etc.

I suspect that there is something wrong with your structure that is causing
a divide by zero somewhere followed by an infinite force and then bang...
That said the code shouldn't segfault. But more detail is needed to track
this down.

All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
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> -----Original Message-----
> From:
> [] On Behalf Of Seth Lilavivat
> Sent: Wednesday, January 10, 2007 11:29
> To:
> Subject: AMBER: sander crashes during minimization
> Dear Amber Community,
> I have been using sander for some time now and this is the
> first encounter of
> the problem. My current setup is as follows:
> AMD 64
> SuSE 10.1
> Amber 8
> iFort
> I have been running many MD simulations on nucleic acid
> stuctures. The latest
> one that I am trying to work results in a segmentation fault
> during the first
> few seconds of the first stage of minimization. I have
> minimized and run MD on
> other models and everything seems to work fine. However,
> with this one the
> error I get is:
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> What are some things I can do to go about solving this problem?
> Thanks,
> --------------------------------------------------------------
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Received on Sun Jan 14 2007 - 06:07:14 PST
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