AMBER Archive (2004)

Subject: Re: AMBER: partition error in shake

From: Scott Brozell (
Date: Tue Apr 27 2004 - 17:26:44 CDT

For closure here is the resolution:

Hi, Scott

I think I know what's going on with the partition error in shake. For a
multi-molecule system, sander assumes/requires that atoms of the same
molecule are in the same block of the PDB file (I don't remember if this
is documented anywhere). But my PDB file has a metal ion bonded to one
of the monomer, but this metal ion is not located in the same block as
the monomer. This created the partition error in shake. Reordering this
atom solved the problem.



Scott Brozell wrote:
> Hi Guanglei,
> This indicates that a constrained pair of atoms are on different
> processors.

On Fri, 23 Apr 2004, Guanglei Cui wrote:

> > After I managed to get SCALI to work with AMBER8, I found I can't use
> > more than 4 CPUs for one of my systems (80,000 atoms), but it worked
> > fine with a regular DNA test case (10 base pairs). It failed because of
> > "partition error in shake". Before I dive into shake.f, I wonder if
> > anyone has a quick guess what might be the problem. Thanks in advance.
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