

AMBER Archive (2006)Subject: Re: AMBER: problem with amber 9 and igb=5 From: M. Scott Shell (shell_at_maxwell.compbio.ucsf.edu)Date: Sat Jun 10 2006  13:40:05 CDT
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 nonreproducability of this problem makes it difficult to diagnose.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. 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 g95compiled code? Scott  The AMBER Mail Reflector To post, send mail to amber@scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo@scripps.edu
 
