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..
Thanks.
Quoting "David A. Case" <case.scripps.edu>:
> On Tue, Feb 01, 2005, Xin Wang wrote:
> >
> > I tried to minimize a huge system containing 860 residues and ~30000
> TIP3P
> > water with sander. I planned to use 500 steepest descent steps
> followed by
> > 500 conjugate gradient steps. However, conjugate gradient never works
> for
> > my system. When the steepest desc. finishes before conj. grad. starts,
> my
> > sander job will exit with a "segmentation fault" message
>
> I don't think you should be seeing this problem. Try some tests with
> the
> system in amber8/benchmarks/rt, which has 141,000 atoms. See if you can
> minimize this on your system. That will help decide if the problem is
> with
> your input files, or with your version of sander.
>
> ...dac
>
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***************
Xin Wang
Pharmacology
UMDNJ
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Received on Wed Feb 02 2005 - 21:53:00 PST
