RE: amber-developers: State of PIMD / NEB test cases.

From: Ross Walker <>
Date: Mon, 30 Apr 2007 08:32:20 -0700

Hi Francesco and other PIMD people...

> Some of the updated PIMD test cases are in the directory
> test/PIMD and
> these are included in the Makefile. I'm going to put also there the
> tests for PIMD/QMMM and PIMD/GB.

Okay - so let me confirm the situation here...

1) All active Amber 10 PIMD test cases are now in the directory

2) All active Amber 10 evb test cases are in the directory

Is this correct?

If so then I assume all of the following test cases are defunct and can be
removed from the CVS tree:


These all look to be empty directories so should probably just be backed up
and removed from the master CVS tree by Dave C.

test/full_pimd (and all sub directories)
test/part_pimd (and all sub directories)

These still contain a large number of active CVS files and were the original
source of my confusion. I suggest all the files get removed from CVS. Dave C
can then backup the attic files and delete the directories from the master
cvs tree.


These all still have active CVS files in but are not run from the Makefile
anymore. This of course means that the code would appear to have been
updated but we now have no active PIMD QMMM test cases. In addition we
actually have NO active NEB test cases either QMMM or classical.

So I assume the above should also be deleted and then Francesco you will
create verified (and I do mean verified, not just copies of the output
files, but calculations where you explicitly verify the results) copies of
QMMM PIMD test cases in the test/PIMD directory?

Meanwhile since we have no active NEB test cases and I am in the process of
trying to explicitly verify the NEB results - by checking that it gets the
correct pathway for alanine dipeptide - I will create a directory called:


and in here I will put a series of classical and QMMM NEB test cases and
these can become the master NEB test cases.

Are we all in agreement here?

If so then I will start going through and cleaning up the above named
directories using "cvs remove"

All the best

|\oss Walker

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| San Diego Supercomputer Center |
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Received on Wed May 02 2007 - 06:07:17 PDT
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