RE: AMBER: problem with amber 9 and igb=5

From: Ross Walker <>
Date: Sat, 10 Jun 2006 12:31:26 -0700

Dear Scott,
Have you checked your hardware? The sorts of problems you are reporting
suggest to me that you may have failing hardware. Do other codes always run
without incident? Do you see the same behaviour in serial as in parallel?
Are the problems correlated with which machines are used to run the job?
All the best

|\oss Walker

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From: [] On Behalf Of
M. Scott Shell
Sent: Saturday, June 10, 2006 11:40
Subject: Re: AMBER: problem with amber 9 and igb=5

David A. Case wrote:

On Thu, Jun 08, 2006, M. Scott Shell wrote:


Given the fact that our minimization was erratic and not entirely

reproducible and knowing that many of our initial pdb configurations had

"perfect" dihedral angles, I decided to perturb all initial pdb phi/psi

angles by a random amount by up to +- 1 degree. As it turns out, this

fixed our problem and we no longer saw amber hanging during minimization.


Weird...I can't offhand think of any reason why amber9 would be different

than earlier versions in this respect. The basic routines that work with

angles and torsions haven't changed for many years.


Well, after further tests, the hanging problem appeared again, so I think I
was just lucky the first time around when I tested it. Unfortunately the
randomness and non-reproducability of this problem makes it difficult to

I decided to take a different strategy and compile with ifort rather than
g95. For the time being, this seemed to do the trick. Has anyone else had
problems with sander minimizations using g95-compiled code?


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Received on Sun Jun 11 2006 - 06:07:21 PDT
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