AMBER Archive (2006)

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

From: M. Scott Shell (
Date: Sat Jun 10 2006 - 13:40:05 CDT

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 diagnose.

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?


----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to