AMBER Archive (2005)

Subject: Re: AMBER: sander segmentation fault

From: Furse, Kristina Elisabet (kristina.e.furse_at_vanderbilt.edu)
Date: Wed Feb 02 2005 - 17:32:25 CST

Out of curiosity along the lines of this thread--I seem to remember (memory
backed up by some old notes...) that in an older version of the DNA tutorial (2
years ago maybe--pre-amber8 release, but post amber7) it suggested you set ncyc
larger than maxcyc for minimizations involving rigid water models like TIP3P and
SPC/E, because conjugate gradient minimization on these rigid models often
resluted in LINEMIN failures. Looking through the current version of the DNA
tutorial today, it suggests more or less half steepest decent and half conjugate
gradient, with no mention of a problem with rigid water. Has something changed
in amber8 or did I misunderstand?
Thanks,
Kristina

Quoting "David A. Case" <case_at_scripps.edu>:

> On Wed, Feb 02, 2005, Xin Wang wrote:
>
> > Thank you for your reply. I found sander could not minimize the system you
> > mentioned below with conjugate gradient either. I am wondering if our
> > amber8 was installed properly or there is any internal limitation for atom
> > number within a system for sander when using conj.grad..
>
> Minimization of the rt system works fine for me. You will have to provide
> information about what OS and compiler you have used. You may also have
> to check smaller systems, to see if there is some obvious limit.
> Also, be sure that your stacksize limit is either "unlimited" or very large.
>
> ....dac
>
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Kristina E. Furse
Department of Chemistry
Center for Structural Biology
Vanderbilt University
Email: kristina.e.furse_at_Vanderbilt.Edu
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