Hi All,
We have a user reporting that sander/sander.mpi work well with Amber12
generated prmtop/inpcrd files, but not with Amber11 generated files.
Portion of his email is enclosed below. I'm also attaching the diff file
between the two prmtop files, which only contains the GB-specific
ATOMIC_NUMBER and SCEE/SCNB sections. The absence of these sections should
all be taken care of by the new sander.
The symptom of the failure is that the system temperature rises very
quickly to thousands of degrees when using the Amber11 generated files as
shown in the attached output file. More interestingly, the failure is
machine dependent. It only occurs on certain local machines. What could be
the cause?
All the best,
Ray
++++
More importantly, Amber12 looks to be working. The only difference was
that I constructed the coordinate and topology files on HPC starting from
scratch with a PDB file. Previously I was constructing these files on
another computer (using Amber 11) and then moving them to HPC. This is the
method I used with stampede and it works fine but not with HPC. This is a
bit inconvenient since all the heme, ligand, etc parameter files need to
be moved to HPC but what I might do is set up directories with all the
non-standard ligands and cofactors on HPC.
++++
--
Ray Luo, Ph.D.
Professor,
Biochemistry, Molecular Biophysics, and
Biomedical Engineering
University of California, Irvine, CA 92697-3900
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- application/octet-stream attachment: diff.out
- application/octet-stream attachment: md1.out
Received on Fri Nov 22 2013 - 12:00:02 PST
